%0 Journal Article %J Molecules %D 2021 %T Synthetic Transition from Thiourea-Based Compounds to Tetrazole Derivatives: Structure and Biological Evaluation of Synthesized New N-(Furan-2-ylmethyl)-1H-tetrazol-5-amine Derivatives %A Daniel Szulczyk %A Anna Bielenica %A Piotr Roszkowski %A Michał A. Dobrowolski %A Wioletta Olejarz %A Sebastian Kmiecik %A Malgorzata Podsiad %A Marta Struga %X Twelve novel derivatives of N-(furan-2-ylmethyl)-1H-tetrazol-5-amine were synthesized. For obtained compound 8, its corresponding substrate single crystals were isolated and X-ray diffraction experiments were completed. In the initial stage of research, in silico structure-based pharmacological prediction was conducted. All compounds were screened for their antibacterial and antimycobacterial activities using standard and clinical strains. The cytotoxic activity was evaluated against a panel of human cancer cell lines, in contrast to normal (HaCaT) cell lines, by using the MTT method. All examined derivatives were found to be noncytotoxic against normal cell lines. Within the studied group, compound 6 showed the most promising results in antimicrobial studies. It inhibited four hospital S. epidermidis rods’ growth, when applied at the amount of 4 µg/mL. However, the most susceptible to the presence of compound 6 was S. epidermidis T 5501 851/19 clinical strain, for which the MIC value was only 2 µg/mL. Finally, a pharmacophore model was established based on lead compounds from this and our previous work. %B Molecules %V 26 %G eng %U https://www.mdpi.com/1420-3049/26/2/323 %R 10.3390/molecules26020323 %0 Journal Article %J Bioinformatics %D 2019 %T CABS-dock standalone: a toolbox for flexible protein-peptide docking %A Maciej Ciemny %A Tymoteusz Oleniecki %A Aleksander Kuriata %A Mateusz Kurcinski %A Aleksandra E. Badaczewska-Dawid %A Andrzej Koliński %A Sebastian Kmiecik %X CABS-dock standalone is a multiplatform Python package for protein-peptide docking with backbone flexibility. The main feature of the CABS-dock method is its ability to simulate significant backbone flexibility of the entire protein-peptide system in a reasonable computational time. In the default mode, the package runs a simulation of fully flexible peptide searching for a binding site on the surface of a flexible protein receptor. The flexibility level of the molecules may be defined by the user. Furthermore, the CABS-dock standalone application provides users with full control over the docking simulation from the initial setup to the analysis of results. The standalone version is an upgrade of the original web server implementation – it introduces a number of customizable options, provides support for large-sized systems and offers a framework for deeper analysis of docking results.CABS-dock standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python and Fortran. The CABS-dock standalone source code, wiki with documentation and examples of use, and installation instructions for Linux, macOS, and Windows are available in the CABS-dock standalone repository at https://bitbucket.org/lcbio/cabsdock %B Bioinformatics %V btz185 %8 03 %G eng %U https://dx.doi.org/10.1093/bioinformatics/btz185 %R 10.1093/bioinformatics/btz185 %0 Journal Article %J Nucleic Acids Research, gky356 %D 2018 %T CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures %A Aleksander Kuriata %A Aleksandra Maria Gierut %A Tymoteusz Oleniecki %A Maciej Ciemny %A Andrzej Koliński %A Mateusz Kurcinski %A Sebastian Kmiecik %X Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2 %B Nucleic Acids Research, gky356 %G eng %0 Journal Article %J Bioinformatics %D 2018 %T CABS-flex standalone: a simulation environment for fast modeling of protein flexibility %A Mateusz Kurcinski %A Tymoteusz Oleniecki %A Maciej Ciemny %A Aleksander Kuriata %A Andrzej Koliński %A Sebastian Kmiecik %X Summary: CABS-flex standalone is a Python package for fast simulations of protein structure flexibility. The package combines simulations of protein dynamics using CABS coarse-grained protein model with the reconstruction of selected models to all-atom representation and analysis of modeling results. CABS-flex standalone is designed to allow for command-line access to the CABS computations and complete control over simulation process. CABS-flex standalone is equipped with features such as: modeling of multimeric and large-size protein systems, contact map visualizations, analysis of similarities to the reference structure and configurable modeling protocol. For instance, the user may modify the simulation parameters, distance restraints, structural clustering scheme or all-atom reconstruction parameters. With these features CABS-flex standalone can be easily incorporated into other methodologies of structural biology. Availability and implementation: CABS-flex standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python. CABS-flex source code, wiki with examples of use and installation instructions for Linux, macOS and Windows are available from the CABS-flex standalone repository at https://bitbucket.org/lcbio/cabsflex %B Bioinformatics %P bty685 %G eng %U http://dx.doi.org/10.1093/bioinformatics/bty685 %R 10.1093/bioinformatics/bty685 %0 Journal Article %J European Journal of Medicinal Chemistry %D 2018 %T Design and synthesis of novel 1H-tetrazol-5-amine based potent antimicrobial agents: DNA topoisomerase IV and gyrase affinity evaluation supported by molecular docking studies %A Daniel Szulczyk %A Michał A. Dobrowolski %A Piotr Roszkowski %A Anna Bielenica %A Joanna Stefańska %A Michal Kolinski %A Sebastian Kmiecik %A Michał Jóźwiak %A Małgorzata Wrzosek %A Wioletta Olejarz %A Marta Struga %K 1H-tetrazol-5-amine %K Antimicrobial activity %K Cytotoxicity %K DNA gyrase %K molecular docking %K Topoisomerase type IV %X A total of 14 of 1,5-disubstituted tetrazole derivatives were prepared by reacting appropriate thiourea and sodium azide in the presence of mercury (II) chloride and triethylamine. All compounds were evaluated in vitro for their antimicrobial activity. Derivatives 10 and 11 showed the highest inhibition against Gram-positive and Gram-negative strains (standard and hospital strains). The observed minimal inhibitory concentrations values were in the range of 1–208 μM (0.25–64 μg/ml). Inhibitory activity of 1,5-tetrazole derivatives 10 and 11 against gyrase and topoisomerase IV isolated from S. aureus was studied. Evaluation was supported by molecular docking studies for all synthesized derivatives and reference ciprofloxacin. Moreover, selected tetrazoles (2, 3, 5, 6, 8, 9, 10 and 11) were evaluated for their cytotoxicity. All tested compounds are non-cytotoxic against HaCaT and A549 cells (CC50 ≤ 60 μM). %B European Journal of Medicinal Chemistry %V 156 %P 631 - 640 %G eng %U http://www.sciencedirect.com/science/article/pii/S022352341830597X %R https://doi.org/10.1016/j.ejmech.2018.07.041 %0 Journal Article %J RSC Advances %D 2017 %T Biofunctionalisation of p-doped silicon with cytochrome c553 minimises charge recombination and enhances photovoltaic performance of the all-solid-state photosystem I-based biophotoelectrode %A Julian David Janna Olmos %A Philippe Becquet %A Dominik Gront %A Jarosław Sar %A Andrzej Dąbrowski %A Grzegorz Gawlik %A Marian Teodorczyk %A Dorota Pawlak %A Joanna Kargul %X Surface-directed passivation of p-doped silicon (Si) substrate was achieved by its biofunctionalisation with hexahistidine (His6)-tagged cytochrome c553 (cyt c553), a soluble electroactive photosynthetic protein responsible for electron donation to photooxidised photosystem I (PSI). Five distinct variants of cyt c553 were genetically engineered by introducing the specific linker peptides of 0–19 amino acids (AA) in length between the cyt c553 holoprotein and a C-terminal His6-tag, the latter being the affinity ‘anchor’ used for the specific immobilisation of this protein on the semiconductor surface. Calculation of 2D Gibbs free energy maps for the five cyt c553 variants showed a significantly higher number of thermodynamically feasible conformations of immobilised cyt c variants containing longer linker peptides. Here we show that the distinct cyt c553-based Si bioelectrodes display some characteristics of the p–n-type diodes, albeit varying in the level of dark saturation current J0 considered as the charge recombination parameter. These combined bioinformatic and electrochemical analyses indicate that the cyt c553 variants with longer linker peptides, up to 19AA in length, allow for more structural flexibility of immobilised cyt c553 in terms of both, orientation and distance of the haem group with respect to the Si surface, and promote the efficient biopassivation of the semiconductor substrate. Incorporation of the specifically immobilised 19AA cyt c553 variant into the all-solid-state biophotoelectrodes containing light harvesting PSI module enhanced biophotovoltaic performance of the PSI biophotoelectrode compared to the analogous device devoid of cyt c553. %B RSC Advances %V 7 %P 47854-47866 %G eng %U http://pubs.rsc.org/en/content/articlepdf/2017/ra/c7ra10895h %R 10.1039/c7ra10895h %0 Journal Article %J Biophysical Journal %D 2014 %T Connecting thermal and mechanical protein (un)folding landscapes %A Li Sun %A Jeffrey K. Noel %A Joanna I. Sulkowska %A Herbert Levine %A José N. Onuchic %X Molecular dynamics simulations supplement single-molecule pulling experiments by providing the possibility of examining the full free energy landscape using many coordinates. Here, we use an all-atom structure-based model to study the force and temperature dependence of the unfolding of the protein filamin by applying force at both termini. The unfolding time-force relation τ(F) indicates that the force-induced unfolding behavior of filamin can be characterized into three regimes: barrier-limited low- and intermediate-force regimes, and a barrierless high-force regime. Slope changes of τ(F) separate the three regimes. We show that the behavior of τ(F) can be understood from a two-dimensional free energy landscape projected onto the extension X and the fraction of native contacts Q. In the low-force regime, the unfolding rate is roughly force-independent due to the small (even negative) separation in X between the native ensemble and transition state ensemble (TSE). In the intermediate-force regime, force sufficiently separates the TSE from the native ensemble such that τ(F) roughly follows an exponential relation. This regime is typically explored by pulling experiments. While X may fail to resolve the TSE due to overlap with the unfolded ensemble just below the folding temperature, the overlap is minimal at lower temperatures where experiments are likely to be conducted. The TSE becomes increasingly structured with force, whereas the average order of structural events during unfolding remains roughly unchanged. The high-force regime is characterized by barrierless unfolding, and the unfolding time approaches a limit of ∼10 μs for the highest forces we studied. Finally, a combination of X and Q is shown to be a good reaction coordinate for almost the entire force range. %B Biophysical Journal %V 107(12) %P 2950-61 %G eng %& 2950 %R 10.1016/j.bpj.2014.10.021 %0 Journal Article %J PLoS computational biology %D 2014 %T Pierced Lasso Bundles are a New Class of Knot Motifs %A Haglund, Ellinor %A Joanna I. Sulkowska %A Noel, Jeffrey K. %A Lammert, H %A Onuchic, José N. %A Jennings, Patricia A %X A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins). We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB) and the knot-like threaded structural motif a Pierced Lasso (PL). In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso) in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets. %B PLoS computational biology %V 10(6) %G eng %& e1003613 %R doi: 10.1371/journal.pcbi.1003613 %0 Journal Article %J Journal of Chemical Theory and Computation %D 2013 %T Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field %A Michal Jamroz %A Modesto Orozco %A Andrzej Koliński %A Sebastian Kmiecik %K molecular dynamics %K near-native dynamics %K protein dynamics %K protein flexibility %K simulation %X It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution. %B Journal of Chemical Theory and Computation %V 9 %P 119 - 125 %8 12/2012 %@ 1549-9618 %G eng %U http://dx.doi.org/10.1021/ct300854w %N 1 %! J. Chem. Theory Comput. %R 10.1021/ct300854w %0 Journal Article %J Journal of Physicak Chemistry Letters %D 2013 %T Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins. %A Andrews, Benjamin T %A Capraro, Dominique T %A Joanna I. Sulkowska %A Onuchic, José N %A Jennings, Patricia A %X Topologically complex proteins fold by multiple routes as a result of hard-to-fold regions of the proteins. Oftentimes these regions are introduced into the protein scaffold for function and increase frustration in the otherwise smooth-funneled landscape. Interestingly, while functional regions add complexity to folding landscapes, they may also contribute to a unique behavior referred to as hysteresis. While hysteresis is predicted to be rare, it is observed in various proteins, including proteins containing a unique peptide cyclization to form a fluorescent chromophore as well as proteins containing a knotted topology in their native fold. Here, hysteresis is demonstrated to be a consequence of the decoupling of unfolding events from the isomerization or hula-twist of a chromophore in one protein and the untying of the knot in a second protein system. The question now is- can hysteresis be a marker for the interplay of landscapes where complex folding and functional regions overlap? %B Journal of Physicak Chemistry Letters %V 4 %P 180-188 %8 2013 Jan 3 %G eng %N 1 %R 10.1021/jz301893w %0 Journal Article %J The Journal of Physical Chemistry Letters %D 2013 %T Knotting a Protein in Explicit Solvent %A Jeffrey K. Noel %A José N. Onuchic %A Joanna I. Sulkowska %X Recently, experiments have confirmed that trefoil knotted proteins can fold spontaneously, consistent with predictions from simulations of simplified protein models. These simulations suggest folding the knot involves threading the protein terminal across a twisted loop via a slipknot configuration. Here, we report unbiased all-atom explicit-solvent simulations of the knotting dynamics of a protein. In simulations totaling 40 μs, we find that 5 out of 15 simulations reach the knotted native state when initiated from unknotted, slipknotted intermediates. The completed threading events had durations of 0.1–2 μs. Comparison of explicit-solvent to structure-based simulations shows that similar native contacts are responsible for threading the slipknot through the loop; however, competition between native and non-native salt bridges during threading results in increased energetic roughness. Overall, these simulations support a slipknotting mechanism for proteins with complex topology, and help verify that simplified models are useful tools for studying knotted proteins. %B The Journal of Physical Chemistry Letters %V 4 %P 3570-3573 %G eng %U http://pubs.acs.org/doi/abs/10.1021/jz401842f %R 10.1021/jz401842f %0 Journal Article %J Biochemical Society Transactions %D 2013 %T Knotting pathways in proteins. %A Joanna I. Sulkowska %A Noel, Jeffrey K %A Ramírez-Sarmiento, César A %A Rawdon, Eric J %A Millett, Kenneth C %A Onuchic, José N %K Animals %K Humans %K Protein Conformation %K Protein Engineering %K Protein Folding %K Proteins %K Thermodynamics %X Most proteins, in order to perform their biological function, have to fold to a compact native state. The increasing number of knotted and slipknotted proteins identified suggests that proteins are able to manoeuvre around topological barriers during folding. In the present article, we review the current progress in elucidating the knotting process in proteins. Although we concentrate on theoretical approaches, where a knotted topology can be unambiguously detected, comparison with experiments is also reviewed. Numerical simulations suggest that the folding process for small knotted proteins is composed of twisted loop formation and then threading by either slipknot geometries or flipping. As the size of the knotted proteins increases, particularly for more deeply threaded termini, the prevalence of traps in the free energy landscape also increases. Thus, in the case of longer knotted and slipknotted proteins, the folding mechanism is probably supported by chaperones. Overall, results imply that knotted proteins can be folded efficiently and survive evolutionary pressure in order to perform their biological functions. %B Biochemical Society Transactions %V 41 %P 523-7 %8 2013 Apr %G eng %N 2 %R 10.1042/BST20120342 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2012 %T Conservation of complex knotting and slipknotting patterns in proteins. %A Joanna I. Sulkowska %A Rawdon, Eric J %A Millett, Kenneth C %A Onuchic, José N %A Stasiak, Andrzej %K Protein Conformation %K Protein Folding %K Proteins %X While analyzing all available protein structures for the presence of knots and slipknots, we detected a strict conservation of complex knotting patterns within and between several protein families despite their large sequence divergence. Because protein folding pathways leading to knotted native protein structures are slower and less efficient than those leading to unknotted proteins with similar size and sequence, the strict conservation of the knotting patterns indicates an important physiological role of knots and slipknots in these proteins. Although little is known about the functional role of knots, recent studies have demonstrated a protein-stabilizing ability of knots and slipknots. Some of the conserved knotting patterns occur in proteins forming transmembrane channels where the slipknot loop seems to strap together the transmembrane helices forming the channel. %B Proceedings of the National Academy of Sciences of the United States of America %V 109 %P E1715-23 %8 2012 Jun 26 %G eng %N 26 %R 10.1073/pnas.1205918109 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2012 %T Energy landscape of knotted protein folding. %A Joanna I. Sulkowska %A Noel, Jeffrey K %A Onuchic, José N %K Evolution, Molecular %K Kinetics %K Models, Molecular %K Molecular Dynamics Simulation %K Mutation %K Protein Folding %K Proteins %X Recent experiments have conclusively shown that proteins are able to fold from an unknotted, denatured polypeptide to the knotted, native state without the aid of chaperones. These experiments are consistent with a growing body of theoretical work showing that a funneled, minimally frustrated energy landscape is sufficient to fold small proteins with complex topologies. Here, we present a theoretical investigation of the folding of a knotted protein, 2ouf, engineered in the laboratory by a domain fusion that mimics an evolutionary pathway for knotted proteins. Unlike a previously studied knotted protein of similar length, we see reversible folding/knotting and a surprising lack of deep topological traps with a coarse-grained structure-based model. Our main interest is to investigate how evolution might further select the geometry and stiffness of the threading region of the newly fused protein. We compare the folding of the wild-type protein to several mutants. Similarly to the wild-type protein, all mutants show robust and reversible folding, and knotting coincides with the transition state ensemble. As observed experimentally, our simulations show that the knotted protein folds about ten times slower than an unknotted construct with an identical contact map. Simulated folding kinetics reflect the experimentally observed rollover in the folding limbs of chevron plots. Successful folding of the knotted protein is restricted to a narrow range of temperature as compared to the unknotted protein and fits of the kinetic folding data below folding temperature suggest slow, nondiffusive dynamics for the knotted protein. %B Proceedings of the National Academy of Sciences of the United States of America %V 109 %P 17783-8 %8 2012 Oct 30 %G eng %N 44 %R 10.1073/pnas.1201804109 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2012 %T Genomics-aided structure prediction. %A Joanna I. Sulkowska %A Morcos, Faruck %A Weigt, Martin %A Hwa, Terence %A Onuchic, José N %K Amino Acid Sequence %K Genomics %K Molecular Dynamics Simulation %K Molecular Sequence Data %K Proteins %K Sequence Homology, Amino Acid %X We introduce a theoretical framework that exploits the ever-increasing genomic sequence information for protein structure prediction. Structure-based models are modified to incorporate constraints by a large number of non-local contacts estimated from direct coupling analysis (DCA) of co-evolving genomic sequences. A simple hybrid method, called DCA-fold, integrating DCA contacts with an accurate knowledge of local information (e.g., the local secondary structure) is sufficient to fold proteins in the range of 1-3 Å resolution. %B Proceedings of the National Academy of Sciences of the United States of America %V 109 %P 10340-5 %8 2012 Jun 26 %G eng %N 26 %R 10.1073/pnas.1207864109 %0 Journal Article %J PLoS One %D 2012 %T The unique cysteine knot regulates the pleotropic hormone leptin. %A Haglund, Ellinor %A Joanna I. Sulkowska %A He, Zhao %A Feng, Gen-Sheng %A Jennings, Patricia A %A Onuchic, José N %K Cysteine %K Humans %K Kinetics %K Leptin %K MCF-7 Cells %K Models, Molecular %K Oxidation-Reduction %K Signal Transduction %X Leptin plays a key role in regulating energy intake/expenditure, metabolism and hypertension. It folds into a four-helix bundle that binds to the extracellular receptor to initiate signaling. Our work on leptin revealed a hidden complexity in the formation of a previously un-described, cysteine-knotted topology in leptin. We hypothesized that this unique topology could offer new mechanisms in regulating the protein activity. A combination of in silico simulation and in vitro experiments was used to probe the role of the knotted topology introduced by the disulphide-bridge on leptin folding and function. Our results surprisingly show that the free energy landscape is conserved between knotted and unknotted protein, however the additional complexity added by the knot formation is structurally important. Native state analyses led to the discovery that the disulphide-bond plays an important role in receptor binding and thus mediate biological activity by local motions on distal receptor-binding sites, far removed from the disulphide-bridge. Thus, the disulphide-bridge appears to function as a point of tension that allows dissipation of stress at a distance in leptin. %B PLoS One %V 7 %P e45654 %8 2012 %G eng %N 9 %R 10.1371/journal.pone.0045654 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2010 %T Slipknotting upon native-like loop formation in a trefoil knot protein. %A Noel, Jeffrey K %A Joanna I. Sulkowska %A Onuchic, José N %K Algorithms %K Archaea %K Archaeal Proteins %K Crystallization %K Databases, Protein %K Models, Molecular %K Molecular Dynamics Simulation %K Protein Conformation %K Protein Folding %K Protein Multimerization %K Protein Structure, Secondary %K Protein Structure, Tertiary %K Thermodynamics %X Protein knots and slipknots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Recent experimental results show that knotting, starting from a fully extended polypeptide, has not yet been observed. Understanding the nucleation process of folding knots is thus a natural challenge for both experimental and theoretical investigation. In this study, we employ energy landscape theory and molecular dynamics to elucidate the entire folding mechanism. The full free energy landscape of a knotted protein is mapped using an all-atom structure-based protein model. Results show that, due to the topological constraint, the protein folds through a three-state mechanism that contains (i) a precise nucleation site that creates a correctly twisted native loop (first barrier) and (ii) a rate-limiting free energy barrier that is traversed by two parallel knot-forming routes. The main route corresponds to a slipknot conformation, a collapsed configuration where the C-terminal helix adopts a hairpin-like configuration while threading, and the minor route to an entropically limited plug motion, where the extended terminus is threaded as through a needle. Knot formation is a late transition state process and results show that random (nonspecific) knots are a very rare and unstable set of configurations both at and below folding temperature. Our study shows that a native-biased landscape is sufficient to fold complex topologies and presents a folding mechanism generalizable to all known knotted protein topologies: knotting via threading a native-like loop in a preordered intermediate. %B Proceedings of the National Academy of Sciences of the United States of America %V 107 %P 15403-8 %8 2010 Aug 31 %G eng %N 35 %R 10.1073/pnas.1009522107 %0 Journal Article %J PLoS Comput Biol %D 2010 %T A Stevedore's protein knot. %A Bölinger, Daniel %A Joanna I. Sulkowska %A Hsu, Hsiao-Ping %A Mirny, Leonid A %A Kardar, Mehran %A Onuchic, José N %A Virnau, Peter %K Databases, Protein %K Hydrolases %K Molecular Dynamics Simulation %K Protein Conformation %K Protein Folding %X Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered alpha-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified protein fragment that consists of only 92 amino acids. The topological complexity of the Stevedore knot presents a puzzle as to how it could possibly fold. To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possible mechanism by which the knot forms in a single loop flip. %B PLoS Comput Biol %V 6 %P e1000731 %8 2010 Apr %G eng %N 4 %R 10.1371/journal.pcbi.1000731 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2009 %T Dodging the crisis of folding proteins with knots. %A Joanna I. Sulkowska %A Sułkowski, Piotr %A Onuchic, José %K Kinetics %K Models, Molecular %K Protein Folding %K Protein Structure, Tertiary %K Proteins %X Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, that involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in approximately 1-2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies. %B Proceedings of the National Academy of Sciences of the United States of America %V 106 %P 3119-24 %8 2009 Mar 3 %G eng %N 9 %R 10.1073/pnas.0811147106 %0 Journal Article %J Phys Rev Lett %D 2009 %T Jamming proteins with slipknots and their free energy landscape. %A Joanna I. Sulkowska %A Sułkowski, Piotr %A Onuchic, José N %K Protein Conformation %K Protein Folding %K Proteins %K Thermodynamics %K Time Factors %X Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative unfolding routes that are dominant at different force ranges. The existence of an intermediate, metastable configuration where the slipknot is jammed is responsible for longer unfolding times at higher forces. Simulations are performed with a coarse-grained model with further quantification using a refined description of the geometry of the slipknots. The simulation data are used to determine the free energy landscape of the protein, which supports recent analytical predictions. %B Phys Rev Lett %V 103 %P 268103 %8 2009 Dec 31 %G eng %N 26 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2009 %T On the remarkable mechanostability of scaffoldins and the mechanical clamp motif. %A Valbuena, Alejandro %A Oroz, Javier %A Hervás, Rubén %A Vera, Andrés Manuel %A Rodríguez, David %A Menéndez, Margarita %A Joanna I. Sulkowska %A Cieplak, Marek %A Carrión-Vázquez, Mariano %K Amino Acid Motifs %K Biotechnology %K Cellulose %K Clostridium thermocellum %K Computer Simulation %K Databases, Protein %K Kinetics %K Microscopy, Atomic Force %K Nanotechnology %K Protein Conformation %K Protein Engineering %K Protein Folding %K Protein Structure, Secondary %K Proteins %K Stress, Mechanical %X Protein mechanostability is a fundamental biological property that can only be measured by single-molecule manipulation techniques. Such studies have unveiled a variety of highly mechanostable modules (mainly of the Ig-like, beta-sandwich type) in modular proteins subjected to mechanical stress from the cytoskeleton and the metazoan cell-cell interface. Their mechanostability is often attributed to a "mechanical clamp" of secondary structure (a patch of backbone hydrogen bonds) fastening their ends. Here we investigate the nanomechanics of scaffoldins, an important family of scaffolding proteins that assembles a variety of cellulases into the so-called cellulosome, a microbial extracellular nanomachine for cellulose adhesion and degradation. These proteins anchor the microbial cell to cellulose substrates, which makes their connecting region likely to be subjected to mechanical stress. By using single-molecule force spectroscopy based on atomic force microscopy, polyprotein engineering, and computer simulations, here we show that the cohesin I modules from the connecting region of cellulosome scaffoldins are the most robust mechanical proteins studied experimentally or predicted from the entire Protein Data Bank. The mechanostability of the cohesin modules studied correlates well with their mechanical kinetic stability but not with their thermal stability, and it is well predicted by computer simulations, even coarse-grained. This extraordinary mechanical stability is attributed to 2 mechanical clamps in tandem. Our findings provide the current upper limit of protein mechanostability and establish shear mechanical clamps as a general structural/functional motif widespread in proteins putatively subjected to mechanical stress. These data have important implications for the scaffoldin physiology and for protein design in biotechnology and nanotechnology. %B Proceedings of the National Academy of Sciences of the United States of America %V 106 %P 13791-6 %8 2009 Aug 18 %G eng %N 33 %R 10.1073/pnas.0813093106 %0 Journal Article %J The Journal of Physical Chemistry A %D 2006 %T Effect of Finite Size on Cooperativity and Rates of Protein Folding†%A Maksim Kouza %A Mai Suan Li %A Edward P. O'Brien %A Chin-Kun Hu %A D. Thirumalai %B The Journal of Physical Chemistry A %V 110 %P 671-676 %G eng %U http://pubs.acs.org/doi/abs/10.1021/jp053770b %R 10.1021/jp053770b %0 Journal Article %J Journal of the American Chemical Society %D 2000 %T Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1 %A Carlos Simmerling %A Matthew R. Lee %A Angel. R. Ortiz %A Andrzej Koliński %A Jeffrey Skolnick %A Peter A. Kollman %X A combined method for the prediction of protein tertiary structures from sequence is presented. This multistep procedure initially uses a simplified approach to protein structure prediction, MONSSTER, that assembles structures from initial extended conformations and scores them. Then, using the lowest-energy low-resolution model as a starting conformation, a detailed atomic model is built and refined using molecular dynamics simulations that employ the locally enhanced sampling (LES) methodology with the particle mesh Ewald (PME) technique for calculation of long-range electrostatic interactions. The combined method is applied to a small disulfide-rich 29-residue protein CMTI-1, a trypsin inhibitor found in squash seeds. Starting with an initial low-resolution model from MONSSTER, which has an rmsd from the native conformation of 3.7 Å (5.0 Å) for Cα atoms (all heavy atoms), LES/PME refinement leads to a structure that is only 2.5 Å (3.3 Å) from native, with a Cα rmsd of only 1.7 Å for residues 5−29. These rmsd values should be compared to Cα rmsd values of 1.2 Å (all residues) or 0.8 Å (residues 5−29) found in PME molecular dynamics simulations that start with the native conformation. %B Journal of the American Chemical Society %V 122 %P 8392–8402 %8 sep %G eng %U http://pubs.acs.org/doi/abs/10.1021/ja993119k %R 10.1021/ja993119k %0 Journal Article %J Proteins: Structure, Function, Bioinformatics %D 2000 %T Derivation of protein-specific pair potentials based on weak sequence fragment similarity %A Jeffrey Skolnick %A Andrzej Koliński %A Angel Ortiz %K knowledge-based potentials %K potential deriva- %K Sequence Analysis %K structure prediction %K Tertiary %K tion %X A method is presented for the derivation of knowledge-based pair potentials that corrects for the various compositions of different proteins. The resulting statistical pair potential is more specific than that derived from previous approaches as assessed by gapless threading results. Additionally, a methodology is presented that interpolates between statistical potentials when no homologous examples to the protein of interest are in the structural database used to derive the potential, to a Go-like potential (in which native interactions are favorable and all nonnative interactions are not) when homologous proteins are present. For cases in which no protein exceeds 30% sequence identity, pairs of weakly homologous interacting fragments are employed to enhance the specificity of the potential. In gapless threading, the mean z score increases from -10.4 for the best statistical pair potential to -12.8 when the local sequence similarity, fragment-based pair potentials are used. Examination of the ab initio structure prediction of four representative globular proteins consistently reveals a qualitative improvement in the yield of structures in the 4 to 6 A rmsd from native range when the fragment-based pair potential is used relative to that when the quasichemical pair potential is employed. This suggests that such protein-specific potentials provide a significant advantage relative to generic quasichemical potentials. %B Proteins: Structure, Function, Bioinformatics %V 38 %P 3–16 %G eng %U http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0134(20000101)38:1%3C3::AID-PROT2%3E3.0.CO;2-S/full %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2000 %T Three-dimensional modeling of and ligand docking to vitamin D receptor ligand binding domain %A Keiko Yamamoto %A Hiroyuki Masuno %A Mihwa Choi %A Kinichi Nakashima %A Tetsuya Taga %A Hiroshi Ooizumi %A Kazuhiko Umesono %A Wanda Sicinska %A Janeen VanHooke %A Hector F. DeLuca %A Sachiko Yamada %X The ligand binding domain of the human vitamin D receptor (VDR) was modeled based on the crystal structure of the retinoic acid receptor. The ligand binding pocket of our VDR model is spacious at the helix 11 site and confined at the β-turn site. The ligand 1α,25-dihydroxyvitamin D3 was assumed to be anchored in the ligand binding pocket with its side chain heading to helix 11 (site 2) and the A-ring toward the β-turn (site 1). Three residues forming hydrogen bonds with the functionally important 1α- and 25-hydroxyl groups of 1α,25-dihydroxyvitamin D3 were identified and confirmed by mutational analysis: the 1α-hydroxyl group is forming pincer-type hydrogen bonds with S237 and R274 and the 25-hydroxyl group is interacting with H397. Docking potential for various ligands to the VDR model was examined, and the results are in good agreement with our previous three-dimensional structure-function theory. %B Proceedings of the National Academy of Sciences %V 97 %P 1467-1472 %G eng %U http://www.pnas.org/content/97/4/1467.abstract %R 10.1073/pnas.020522697 %0 Journal Article %J Proteins %D 1999 %T Ab initio folding of proteins using restraints derived from evolutionary information %A Angel. R. Ortiz %A Andrzej Koliński %A Piotr Rotkiewicz %A Bartosz Ilkowski %A Jeffrey Skolnick %K Algorithms %K Amino Acid Sequence %K Evolution %K Models %K Molecular %K Molecular Sequence Data %K Monte Carlo Method %K Protein Folding %K Proteins %K Proteins: chemistry %X We present our predictions in the ab initio structure prediction category of CASP3. Eleven targets were folded, using a method based on a Monte Carlo search driven by secondary and tertiary restraints derived from multiple sequence alignments. Our results can be qualitatively summarized as follows: The global fold can be considered "correct" for targets 65 and 74, "almost correct" for targets 64, 75, and 77, "half-correct" for target 79, and "wrong" for targets 52, 56, 59, and 63. Target 72 has not yet been solved experimentally. On average, for small helical and alpha/beta proteins (on the order of 110 residues or smaller), the method predicted low resolution structures with a reasonably good prediction of the global topology. Most encouraging is that in some situations, such as with target 75 and, particularly, target 77, the method can predict a substantial portion of a rare or even a novel fold. However, the current method still fails on some beta proteins, proteins over the 110-residue threshold, and sequences in which only a poor multiple sequence alignment can be built. On the other hand, for small proteins, the method gives results of quality at least similar to that of threading, with the advantage of not being restricted to known folds in the protein database. Overall, these results indicate that some progress has been made on the ab initio protein folding problem. Detailed information about our results can be obtained by connecting to http:/(/)www.bioinformatics.danforthcenter.org/+ ++CASP3. %B Proteins %V Suppl. 3 %P 177–185 %8 jan %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/10526366 %0 Book Section %B Theoretical and Computational Chemistry: Computational Molecular Biology %D 1999 %T Application of reduced models to protein structure prediction %A Jeffrey Skolnick %A Andrzej Koliński %A Angel. R. Ortiz %X This chapter describes the state of the art of contemporary approaches to protein tertiary structure prediction, and focuses on reduced models. Any successful tertiary structure prediction algorithm must address two intertwined issues: first, it is required to have an energy or fitness function that distinguishes the native conformation from the sea of alternative structures. Second, it must have a conformational search protocol that can find the native conformation among the possible alternative structures. A key issue that is faced when embarking on a program of protein structure prediction is deciding on the level of detail of protein representation. The advantage of a lattice is purely computational. Because the protein is confined to a set of grid points, many geometric and energetic properties can be precalculated in advance. Thus, a well-designed lattice model is about a factor of 10 to 100 times faster than the corresponding continuous space model. %B Theoretical and Computational Chemistry: Computational Molecular Biology %I Elsevier %C Amsterdam %V 8 %P 397–440 %G eng %U http://www.sciencedirect.com/science/article/pii/S1380732399800867 %& 11 %0 Conference Proceedings %B Impact of Advances in Computing and Communications Technologies on Chemical Sciences and Technology, Proceedings of the National Research Council %D 1999 %T The role of computational biology in the genomics revolution %A Jeffrey Skolnick %A Jacquelyn S. Fetrow %A Angel. R. Ortiz %A Andrzej Koliński %B Impact of Advances in Computing and Communications Technologies on Chemical Sciences and Technology, Proceedings of the National Research Council %I National Academy Press %C Washington, D.C. %V pp %P 44–61 %G eng %U http://www.ncbi.nlm.nih.gov/books/NBK44980/ %0 Conference Proceedings %B Proceedings of the Pacific Symposium on Biocomputing ’98 %D 1998 %T Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins %A Angel. R. Ortiz %A Andrzej Koliński %A Jeffrey Skolnick %X By incorporating predicted secondary and tertiary restraints into ab initio folding simulations, low resolution tertiary structures of a test set of 20 nonhomologous proteins have been predicted. These proteins, which represent all secondary structural classes, contain from 37 to 100 residues. Secondary structural restraints are provided by the PHD secondary structure prediction algorithm that incorporates multiple sequence information. Predicted tertiary restraints are obtained from multiple sequence alignments via a two-step process: First, "seed" side chain contacts are identified from a correlated mutation analysis, and then, the seed contacts are "expanded" by an inverse folding algorithm. These predicted restraints are then incorporated into a lattice based, reduced protein model. Depending upon fold complexity, the resulting nativelike topologies exhibit a coordinate root-mean-square deviation, cRMSD, from native between 3.1 and 6.7 A. Overall, this study suggests that the use of restraints derived from multiple sequence alignments combined with a fold assembly algorithm is a promising approach to the prediction of the global topology of small proteins. %B Proceedings of the Pacific Symposium on Biocomputing ’98 %V pp %P 377–388 %G eng %U http://ub.cbm.uam.es/publications/downloads/pdfs/9697197.pdf %0 Journal Article %J Journal of Molecular Biology %D 1998 %T Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments %A Angel. R. Ortiz %A Andrzej Koliński %A Jeffrey Skolnick %K Amino Acid Sequence %K Chemical %K Models %K Molecular Sequence Data %K Monte Carlo Method %K Protein Folding %K Protein Structure %K Secondary %K Tertiary %X The feasibility of predicting the global fold of small proteins by incorporating predicted secondary and tertiary restraints into ab initio folding simulations has been demonstrated on a test set comprised of 20 non-homologous proteins, of which one was a blind prediction of target 42 in the recent CASP2 contest. These proteins contain from 37 to 100 residues and represent all secondary structural classes and a representative variety of global topologies. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that incorporates multiple sequence information. Predicted tertiary restraints are derived from multiple sequence alignments via a two-step process. First, seed side-chain contacts are identified from correlated mutation analysis, and then a threading-based algorithm is used to expand the number of these seed contacts. A lattice-based reduced protein model and a folding algorithm designed to incorporate these predicted restraints is described. Depending upon fold complexity, it is possible to assemble native-like topologies whose coordinate root-mean-square deviation from native is between 3.0 A and 6.5 A. The requisite level of accuracy in side-chain contact map prediction can be roughly 25% on average, provided that about 60% of the contact predictions are correct within +/-1 residue and 95% of the predictions are correct within +/-4 residues. Precision in tertiary contact prediction is more critical than absolute accuracy. Furthermore, only a subset of the tertiary contacts, on the order of 25% of the total, is sufficient for successful topology assembly. Overall, this study suggests that the use of restraints derived from multiple sequence alignments combined with a fold assembly algorithm holds considerable promise for the prediction of the global topology of small proteins. %B Journal of Molecular Biology %V 277 %P 419–448 %8 mar %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/9514747 %R 10.1006/jmbi.1997.1595 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 1998 %T Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations %A Angel. R. Ortiz %A Andrzej Koliński %A Jeffrey Skolnick %K Algorithms %K Models %K Molecular %K Monte Carlo Method %K Protein Folding %K Protein Structure %K Secondary %K Sequence Alignment %K Software %K Tertiary %X By incorporating predicted secondary and tertiary restraints derived from multiple sequence alignments into ab initio folding simulations, it has been possible to assemble native-like tertiary structures for a test set of 19 nonhomologous proteins ranging from 29 to 100 residues in length and representing all secondary structural classes. Secondary structural restraints are provided by the PHD secondary structure prediction algorithm that incorporates multiple sequence information. Multiple sequence alignments also provide predicted tertiary restraints via a two-step process: First, seed side chain contacts are selected from a correlated mutation analysis, and then an inverse folding algorithm expands these seed contacts. The predicted secondary and tertiary restraints are incorporated into a lattice-based, reduced protein model for structure assembly and refinement. The resulting native-like topologies exhibit a coordinate root-mean-square deviation from native for the whole chain between 3.1 and 6.7 A, with values ranging from 2.6 to 4.1 A over approximately 80% of the structure. Overall, this study suggests that the use of restraints derived from multiple sequence alignments combined with a fold assembly algorithm is a promising approach to the prediction of the global topology of small proteins. %B Proceedings of the National Academy of Sciences of the United States of America %V 95 %P 1020–1025 %8 feb %G eng %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=18658&tool=pmcentrez&rendertype=abstract %0 Journal Article %J Journal of Biomolecular Structure and Dynamics %D 1998 %T Reduced protein models and their application to the protein folding problem %A Jeffrey Skolnick %A Andrzej Koliński %A Angel. R. Ortiz %X One of the most important unsolved problems of computational biology is prediction of the three-dimensional structure of a protein from its amino acid sequence. In practice, the solution to the protein folding problem demands that two interrelated problems be simultaneously addressed. Potentials that recognize the native state from the myriad of misfolded conformations are required, and the multiple minima conformational search problem must be solved. A means of partly surmounting both problems is to use reduced protein models and knowledge-based potentials. Such models have been employed to elucidate a number of general features of protein folding, including the nature of the energy landscape, the factors responsible for the uniqueness of the native state and the origin of the two-state thermodynamic behavior of globular proteins. Reduced models have also been used to predict protein tertiary and quaternary structure. When combined with a limited amount of experimental information about secondary and tertiary structure, molecules of substantial complexity can be assembled. If predicted secondary structure and tertiary restraints are employed, low resolution models of single domain proteins can be successfully predicted. Thus, simplified protein models have played an important role in furthering the understanding of the physical properties of proteins. %B Journal of Biomolecular Structure and Dynamics %V 16 %P 381–396 %G eng %U http://www.tandfonline.com/doi/abs/10.1080/07391102.1998.10508255 %0 Journal Article %J Proteins %D 1998 %T Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments %A Angel. R. Ortiz %A Andrzej Koliński %A Jeffrey Skolnick %K Algorithms %K Amino Acid Sequence %K CREB-Binding Protein %K Databases as Topic %K Models %K Molecular %K Molecular Sequence Data %K Monte Carlo Method %K Mutation %K Mutation: genetics %K Nuclear Proteins %K Nuclear Proteins: chemistry %K Protein Folding %K Protein Structure %K Secondary %K Sequence Alignment %K Tertiary %K Trans-Activators %K Transcription Factors %K Transcription Factors: chemistry %X Using a recently developed protein folding algorithm, a prediction of the tertiary structure of the KIX domain of the CREB binding protein is described. The method incorporates predicted secondary and tertiary restraints derived from multiple sequence alignments in a reduced protein model whose conformational space is explored by Monte Carlo dynamics. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that was modified for the presence of predicted U-turns, i.e., regions where the chain reverses global direction. Tertiary restraints are obtained via a two-step process: First, seed side-chain contacts are identified from a correlated mutation analysis, and then, a threading-based algorithm expands the number of these seed contacts. Blind predictions indicate that the KIX domain is a putative three-helix bundle, although the chirality of the bundle could not be uniquely determined. The expected root-mean-square deviation for the correct chirality of the KIX domain is between 5.0 and 6.2 A. This is to be compared with the estimate of 12.9 A that would be expected by a random prediction, using the model of F. Cohen and M. Sternberg (J. Mol. Biol. 138:321-333, 1980). %B Proteins %V 30 %P 287–294 %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/9517544 %0 Conference Proceedings %B Proceeding of II-nd Pacific Symposium on Biocomputing %D 1997 %T Method for low resolution prediction of small protein tertiary structure %A Angel. R. Ortiz %A Wei-Ping Hu %A Andrzej Koliński %A Jeffrey Skolnick %X A new method for the de novo prediction of protein structures at low resolution has been developed. Starting from a multiple sequence alignment, protein secondary structure is predicted, and only those topological elements with high reliability are selected. Then, the multiple sequence alignment and the secondary structure prediction are combined to predict side chain contacts. Such contact map prediction is carried out in two stages. First, an analysis of correlated mutations is carried out to identify pairs of topological elements of secondary structure which are in contact. Then, inverse folding is used to select compatible fragments in contact, thereby enriching the number and identity of predicted side chain contacts. The final outcome of the procedure is a set of noisy secondary and tertiary restraints. These are used as a restrained potential in a Monte Carlo simulation of simplified protein models driven by statistical potentials. Low energy structures are then searched for by using simulated annealing techniques. Implementation of the restraints is carried out so as to take into account of their low resolution. Using this procedure, it has been possible to predict de novo the structure of three very different protein topologies: an alpha/beta protein, the bovine pancreatic trypsin inhibitor (6pti), an alpha-helical protein, calbindin (3icb), and an all beta- protein, the SH3 domain of spectrin (1shg). In all cases, low resolution folds have been obtained with a root mean square deviation (RMSD) of 4.5-5.5 A with respect to the native structure. Some misfolded topologies appear in the simulations, but it is possible to select the native one on energetic grounds. Thus, it is demonstrated that the methodology is general for all protein motifs. Work is in progress in order to test the methodology on a larger set of protein structures. %B Proceeding of II-nd Pacific Symposium on Biocomputing %I World Scientific %P 316–327 %G eng %U http://helix-web.stanford.edu/psb97/ortiz.pdf %0 Journal Article %J Journal of Molecular Biology %D 1997 %T MONSSTER: a method for folding globular proteins with a small number of distance restraints %A Jeffrey Skolnick %A Andrzej Koliński %A Angel. R. Ortiz %K Algorithms %K Aprotinin %K Aprotinin: chemistry %K Bacterial Proteins %K Bacterial Proteins: chemistry %K Computer Graphics %K Computer Simulation %K Flavodoxin %K Flavodoxin: chemistry %K Models %K Molecular %K Myoglobin %K Myoglobin: chemistry %K Plastocyanin %K Plastocyanin: chemistry %K Protein Conformation %K Protein Folding %K Protein Structure %K Secondary %K Tertiary %K Thioredoxins %K Thioredoxins: chemistry %X The MONSSTER (MOdeling of New Structures from Secondary and TEritary Restraints) method for folding of proteins using a small number of long-distance restraints (which can be up to seven times less than the total number of residues) and some knowledge of the secondary structure of regular fragments is described. The method employs a high-coordination lattice representation of the protein chain that incorporates a variety of potentials designed to produce protein-like behaviour. These include statistical preferences for secondary structure, side-chain burial interactions, and a hydrogen-bond potential. Using this algorithm, several globular proteins (1ctf, 2gbl, 2trx, 3fxn, 1mba, 1pcy and 6pti) have been folded to moderate-resolution, native-like compact states. For example, the 68 residue 1ctf molecule having ten loosely defined, long-range restraints was reproducibly obtained with a C alpha-backbone root-mean-square deviation (RMSD) from native of about 4. A. Flavodoxin with 35 restraints has been folded to structures whose average RMSD is 4.28 A. Furthermore, using just 20 restraints, myoglobin, which is a 146 residue helical protein, has been folded to structures whose average RMSD from native is 5.65 A. Plastocyanin with 25 long-range restraints adopts conformations whose average RMSD is 5.44 A. Possible applications of the proposed approach to the refinement of structures from NMR data, homology model-building and the determination of tertiary structure when the secondary structure and a small number of restraints are predicted are briefly discussed. %B Journal of Molecular Biology %V 265 %P 217–241 %8 jan %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/9020984 %R 10.1006/jmbi.1996.0720 %0 Journal Article %J Protein Engineering %D 1996 %T Does a backwardly read protein sequence have a unique native state? %A Krzysztof A. Olszewski %A Andrzej Koliński %A Jeffrey Skolnick %K Amino Acid Sequence %K Computer Simulation %K Models %K Molecular %K Molecular Sequence Data %K Monte Carlo Method %K Protein Conformation %K Protein Engineering %K Protein Folding %K Protein Structure %K Secondary %K Staphylococcal Protein A %K Staphylococcal Protein A: chemistry %K Tertiary %X Amino acid sequences of native proteins are generally not palindromic. Nevertheless, the protein molecule obtained as a result of reading the sequence backwards, i.e. a retro-protein, obviously has the same amino acid composition and the same hydrophobicity profile as the native sequence. The important questions which arise in the context of retro-proteins are: does a retro-protein fold to a well defined native-like structure as natural proteins do and, if the answer is positive, does a retro-protein fold to a structure similar to the native conformation of the original protein? In this work, the fold of retro-protein A, originated from the retro-sequence of the B domain of Staphylococcal protein A, was studied. As a result of lattice model simulations, it is conjectured that the retro-protein A also forms a three-helix bundle structure in solution. It is also predicted that the topology of the retro-protein A three-helix bundle is that of the native protein A, rather than that corresponding to the mirror image of native protein A. Secondary structure elements in the retro-protein do not exactly match their counterparts in the original protein structure; however, the amino acid side chain contract pattern of the hydrophobic core is partly conserved. %B Protein Engineering %V 9 %P 5–14 %8 jan %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/9053902 %0 Journal Article %J Proteins %D 1996 %T Folding simulations and computer redesign of protein A three-helix bundle motifs %A Krzysztof A. Olszewski %A Andrzej Koliński %A Jeffrey Skolnick %K Computer Simulation %K Monte Carlo Method %K Mutation %K Protein Conformation %K Protein Folding %K Staphylococcal Protein A %K Staphylococcal Protein A: chemistry %X In solution, the B domain of protein A from Staphylococcus aureus (B domain) possesses a three-helix bundle structure. This simple motif has been previously reproduced by Kolinski and Skolnick (Proteins 18: 353-366, 1994) using a reduced representation lattice model of proteins with a statistical interaction scheme. In this paper, an improved version of the potential has been used, and the robustness of this result has been tested by folding from the random state a set of three-helix bundle proteins that are highly homologous to the B domain of protein A. Furthermore, an attempt to redesign the B domain native structure to its topological mirror image fold has been made by multiple mutations of the hydrophobic core and the turn region between helices I and II. A sieve method for scanning a large set of mutations to search for this desired property has been proposed. It has been shown that mutations of native B domain hydrophobic core do not introduce significant changes in the protein motif. Mutations in the turn region were also very conservative; nevertheless, a few mutants acquired the desired topological mirror image motif. A set of all atom models of the most probable mutant was reconstructed from the reduced models and refined using a molecular dynamics algorithm in the presence of water. The packing of all atom structures obtained corroborates the lattice model results. We conclude that the change in the handedness of the turn induced by the mutations, augmented by the repacking of hydrophobic core and the additional burial of the second helix N-cap side chain, are responsible for the predicted preferential adoption of the mirror image structure. %B Proteins %V 25 %P 286–299 %8 jul %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/8844865 %R 10.1002/(SICI)1097-0134(199607)25:3<286::AID-PROT2>3.0.CO;2-E %0 Journal Article %J Acta Physica Polonica %D 1989 %T Combinatorial Entropy of Dense Systems of n-mers. The Effect of Shape Studied by Monte Carlo Method %A Andrzej Koliński %A Krzysztof Kurcinski %A Andrzej Orszagh %B Acta Physica Polonica %V 75 %P 879-890 %G eng %0 Journal Article %J Polimery %D 1981 %T Badanie modelu rozgalezionej makroczasteczki metoda Monte Carlo. I. Statystyka konformacyjna (Monte Carlo Study of Star-branched Macromolecules by Means of the Monte Carlo Method. I. Conformational Statistics) %A Andrzej Orszagh %A Andrzej Koliński %A Andrzej Sikorski %B Polimery %V 26 %P 335-337 %G eng %0 Journal Article %J Polimery %D 1981 %T Badanie modelu rozgalezionej makroczasteczki metoda Monte Carlo. II. Rozmiary klebka statystycznego (Monte Carlo Study of Star-branched Macromolecules by Means of the Monte Carlo Method. II. Analysis of the Coil Dimensions) %A Andrzej Orszagh %A Andrzej Koliński %A Andrzej Sikorski %B Polimery %V 26 %P 375-377 %G eng %0 Journal Article %J Acta Physica Polonica %D 1981 %T Monte Carlo Study of Concentrated Polymer Solutions %A Andrzej Orszagh %A Andrzej Koliński %A Jadwiga Duda %B Acta Physica Polonica %V A59 %P 839 %G eng %0 Journal Article %J Acta Physica Polonica %D 1980 %T Monte Carlo Method for Statistical Thermodynamics of Polymer Chains %A Andrzej Orszagh %A Jadwiga Les %A Andrzej Koliński %B Acta Physica Polonica %V A58 %P 369-375 %G eng %0 Journal Article %J Polimery %D 1980 %T Stochastyczna symulacja rodnikowej polimeryzacji w roztworze (Stochastic Simulation of the Free-radical Polymerization in Solution) %A Andrzej Orszagh %E Andrzej Koliński %B Polimery %V 25 %P 124-127 %G eng %0 Journal Article %J Polymer %D 1979 %T Computer Modeling of Radiation-Induced in-Source Solid-State Polymerizations %A Andrzej Orszagh %A Andrzej Koliński %A Piotr Romiszowski %B Polymer %V 20 %P 113 %G eng %0 Journal Article %J Polimery %D 1978 %T Zastosowanie metody Monte Carlo do badania rozmiarow klebka makromolekularnego w roztworze (Application of the Monte Carlo Method in Studying the Macromolecular Coil Dimensions in Solution) %A Andrzej Orszagh %E Andrzej Koliński %Y Jadwiga Les %B Polimery %V 23 %P 207 %G eng %0 Journal Article %J Polimery %D 1977 %T Komputerowa symulacja roztworu polimeru metoda Monte Carlo (Computer Simulation of Polymer Solution by Means of the Monte Carlo Method) %A Andrzej Orszagh %E Andrzej Koliński %Y Jadwiga Les %B Polimery %V 22 %P 444 %G eng