%0 Journal Article %J Nucleic Acids Research %D 2019 %T Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility %A Aleksander Kuriata %A Valentin Iglesias %A Jordi Pujols %A Mateusz Kurcinski %A Sebastian Kmiecik %A Salvador Ventura %X Protein aggregation is a hallmark of a growing number of human disorders and constitutes a major bottleneck in the manufacturing of therapeutic proteins. Therefore, there is a strong need of in-silico methods that can anticipate the aggregative properties of protein variants linked to disease and assist the engineering of soluble protein-based drugs. A few years ago, we developed a method for structure-based prediction of aggregation properties that takes into account the dynamic fluctuations of proteins. The method has been made available as the Aggrescan3D (A3D) web server and applied in numerous studies of protein structure-aggregation relationship. Here, we present a major update of the A3D web server to version 2.0. The new features include: extension of dynamic calculations to significantly larger and multimeric proteins, simultaneous prediction of changes in protein solubility and stability upon mutation, rapid screening for functional protein variants with improved solubility, a REST-ful service to incorporate A3D calculations in automatic pipelines, and a new, enhanced web server interface. A3D 2.0 is freely available at: http://biocomp.chem.uw.edu.pl/A3D2/ %B Nucleic Acids Research %V 47 %P W300-W307 %8 05 %G eng %U https://doi.org/10.1093/nar/gkz321 %R 10.1093/nar/gkz321 %0 Journal Article %J Bioinformatics %D 2019 %T Aggrescan3D standalone package for structure-based prediction of protein aggregation properties %A Aleksander Kuriata %A Valentin Iglesias %A Mateusz Kurcinski %A Salvador Ventura %A Sebastian Kmiecik %X SUMMARY: Aggrescan3D (A3D) standalone is a multiplatform Python package for structure-based prediction of protein aggregation properties and rational design of protein solubility. A3D allows the redesign of protein solubility by combining structural aggregation propensity and stability predictions, as demonstrated by a recent experimental study. It also enables predicting the impact of protein conformational fluctuations on the aggregation properties. The standalone A3D version is an upgrade of the original web server implementation - it introduces a number of customizable options, automated analysis of multiple mutations and offers a flexible computational framework for merging it with other computational tools. AVAILABILITY: A3D standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python. The A3D standalone source code, wiki with documentation and examples of use, and installation instructions for Linux, macOS, and Windows are available in the A3D standalone repository at https://bitbucket.org/lcbio/aggrescan3d. %B Bioinformatics %V btz143 %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/30825368 %9 Journal Article %R 10.1093/bioinformatics/btz143 %0 Journal Article %J Journal of Biotechnology %D 2015 %T Improving thermal stability of thermophilic l-threonine aldolase from Thermotoga maritima. %A Lukasz Wieteska %A Maksim Ionov %A Janusz Szemraj %A Claudia Feller %A Andrzej Koliński %A Dominik Gront %X Threonine aldolase (TA) catalyzes a reversible reaction, in which threonine is decomposed into glycine and acetaldehyde. The same enzyme can be used to catalyze aldol reaction between glycine and a variety of aromatic and aliphatic aldehydes, thus creating various alpha-amino-alcohols. Therefore, TA is a very promising enzyme that could be used to prepare biologically active compounds or building blocks for pharmaceutical industry. Rational design was applied to thermophilic TA from Thermotoga maritima to improve thermal stability by the incorporation of salt and disulfide bridges between subunits in the functional tetramer. An activity assay together with CD analysis and Western-blot detection was used to evaluate mutants. Except one, each of the designed mutants preserved activity toward the natural substrate. One of the 10 proposed single point mutants, P56C, displayed significantly enhanced stability compared to the wild type (WT). Its initial activity was not affected and persisted longer than WT, proportionally to increased stability. Additionally one of the mutants, W86E, displayed enhanced activity, with stability similar to WT. Higher activity may be explained by a subtle change in active site availability. Salt bridge formation between glutamic acid at position 86 and arginine at position 120 in the neighboring chain may be responsible for the slight shift of the chain fragment, thus creating wider access to the active site both for the substrate and PLP. %B Journal of Biotechnology %V 199 %P 69-76 %8 2015 Feb 19 %G eng %R 10.1016/j.jbiotec.2015.02.013 %0 Journal Article %J BMC Structural Biology %D 2007 %T Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily %A Elena M. Ibryashkina %A Marina V. Zakharova %A Vladimir B. Baskunov %A Ekaterina S. Bogdanova %A Maxim O. Nagornykh %A Marat M Den'mukhamedov %A Bogdan S. Melnik %A Andrzej Koliński %A Dominik Gront %A Marcin Feder %A Alexander S. Solonin %A Janusz M. Bujnicki %K Amino Acid Sequence %K Binding Sites %K Computational Biology %K Computational Biology: methods %K Deoxyribonucleases %K DNA %K DNA Cleavage %K DNA: metabolism %K Electrophoretic Mobility Shift Assay %K Models %K Molecular %K Molecular Sequence Data %K Mutation %K Protein %K Protein Conformation %K Sequence Alignment %K Structural Homology %K Type II Site-Specific %K Type II Site-Specific: chemist %K Type II Site-Specific: metabol %X BACKGROUND: The majority of experimentally determined crystal structures of Type II restriction endonucleases (REases) exhibit a common PD-(D/E)XK fold. Crystal structures have been also determined for single representatives of two other folds: PLD (R.BfiI) and half-pipe (R.PabI), and bioinformatics analyses supported by mutagenesis suggested that some REases belong to the HNH fold. Our previous bioinformatic analysis suggested that REase R.Eco29kI shares sequence similarities with one more unrelated nuclease superfamily, GIY-YIG, however so far no experimental data were available to support this prediction. The determination of a crystal structure of the GIY-YIG domain of homing endonuclease I-TevI provided a template for modeling of R.Eco29kI and prompted us to validate the model experimentally. RESULTS: Using protein fold-recognition methods we generated a new alignment between R.Eco29kI and I-TevI, which suggested a reassignment of one of the putative catalytic residues. A theoretical model of R.Eco29kI was constructed to illustrate its predicted three-dimensional fold and organization of the active site, comprising amino acid residues Y49, Y76, R104, H108, E142, and N154. A series of mutants was constructed to generate amino acid substitutions of selected residues (Y49A, R104A, H108F, E142A and N154L) and the mutant proteins were examined for their ability to bind the DNA containing the Eco29kI site 5'-CCGCGG-3' and to catalyze the cleavage reaction. Experimental data reveal that residues Y49, R104, E142, H108, and N154 are important for the nuclease activity of R.Eco29kI, while H108 and N154 are also important for specific DNA binding by this enzyme. CONCLUSION: Substitutions of residues Y49, R104, H108, E142 and N154 predicted by the model to be a part of the active site lead to mutant proteins with strong defects in the REase activity. These results are in very good agreement with the structural model presented in this work and with our prediction that R.Eco29kI belongs to the GIY-YIG superfamily of nucleases. Our study provides the first experimental evidence for a Type IIP REase that does not belong to the PD-(D/E)XK or HNH superfamilies of nucleases, and is instead a member of the unrelated GIY-YIG superfamily. %B BMC Structural Biology %V 7 %P 48 %8 jan %@ 1472680774 %G eng %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1952068&tool=pmcentrez&rendertype=abstract %R 10.1186/1472-6807-7-48 %0 Journal Article %J Macromolecular Theory and Simulations %D 2000 %T Helix-coil and beta sheet-coil transitions in a simplified, yet realistic protein model %A Bartosz Ilkowski %A Jeffrey Skolnick %A Andrzej Koliński %X

A reduced model of polypeptide chains and protein stochastic dynamics is employed in Monte Carlo studies of the coil-globule transition. The model assumes a high-resolution lattice representation of protein conformational space. The interaction scheme is derived from a statistical analysis of structural regularities seen in known three-dimensional protein structures. It is shown that model polypeptides containing residues that have strong propensities towards locally expanded conformations collapse to β-like globular conformations, while polypeptides containing residues with helical propensities form globules of closely packed helices. A more cooperative transition is observed for β-type systems. It is also demonstrated that hydrogen bonding is an important factor for protein cooperativity, although, for systems with suppressed hydrogen bond interactions, a higher cooperativity of β-type proteins is also observed.

%B Macromolecular Theory and Simulations %V 9 %P 523–533 %8 nov %G eng %U http://doi.wiley.com/10.1002/1521-3919(20001101)9:8<523::AID-MATS523>3.0.CO;2-I %N 8 %R 10.1002/1521-3919(20001101)9:8<523::AID-MATS523>3.0.CO;2-I %0 Journal Article %J Progress of Theoretical Physics Supplement %D 2000 %T Protein Folding: Flexible Lattice Models %A Andrzej Koliński %A Piotr Rotkiewicz %A Bartosz Ilkowski %A Jeffrey Skolnick %X In the post genomic era a possibility of theoretical prediction of protein structure from sequence of amino acids is one of the most important and challenging goals of molecular biology. High complexity of the problem requires simplification of molecular models and very efficient computational tools. Proposed here model of protein structure, dynamics and interaction scheme assumes a single interaction center per amino acid residue. This highly simplified representation is supplemented by a number of build-in implicit packing rules that enable a reasonable modeling of protein geometry that is compatible with detailed atomic models. Preliminary applications to ab initio protein folding and distant homology comparative modeling are described and discussed. %B Progress of Theoretical Physics Supplement %V 138 %P 292–300 %G eng %U http://ptp.ipap.jp/link?PTPS/138/292/ %R 10.1143/PTPS.138.292 %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 Journal Article %J Biophysical Journal %D 1999 %T Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques %A Andrzej Koliński %A Bartosz Ilkowski %A Jeffrey Skolnick %K Amino Acid Sequence %K Animals %K Biophysical Phenomena %K Biophysics %K Models %K Molecular %K Molecular Sequence Data %K Monte Carlo Method %K Nerve Tissue Proteins %K Nerve Tissue Proteins: chemistry %K Protein Conformation %K Protein Folding %K Protein Structure %K Proteins %K Proteins: chemistry %K Secondary %K Thermodynamics %X Small peptides that might have some features of globular proteins can provide important insights into the protein folding problem. Two simulation methods, Monte Carlo Dynamics (MCD), based on the Metropolis sampling scheme, and Entropy Sampling Monte Carlo (ESMC), were applied in a study of a high-resolution lattice model of the C-terminal fragment of the B1 domain of protein G. The results provide a detailed description of folding dynamics and thermodynamics and agree with recent experimental findings (. Nature. 390:196-197). In particular, it was found that the folding is cooperative and has features of an all-or-none transition. Hairpin assembly is usually initiated by turn formation; however, hydrophobic collapse, followed by the system rearrangement, was also observed. The denatured state exhibits a substantial amount of fluctuating helical conformations, despite the strong beta-type secondary structure propensities encoded in the sequence. %B Biophysical Journal %V 77 %P 2942–52 %8 dec %G eng %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1300567&tool=pmcentrez&rendertype=abstract %R 10.1016/S0006-3495(99)77127-4 %0 Journal Article %J Proteins %D 1999 %T A method for the improvement of threading-based protein models %A Andrzej Koliński %A Piotr Rotkiewicz %A Bartosz Ilkowski %A Jeffrey Skolnick %K Amino Acid Sequence %K Computer Simulation %K Evaluation Studies as Topic %K Methods %K Models %K Molecular %K Molecular Sequence Data %K Protein Conformation %K Protein Structure %K Proteins %K Proteins: chemistry %K Secondary %K Sequence Alignment %K Software Design %X A new method for the homology-based modeling of protein three-dimensional structures is proposed and evaluated. The alignment of a query sequence to a structural template produced by threading algorithms usually produces low-resolution molecular models. The proposed method attempts to improve these models. In the first stage, a high-coordination lattice approximation of the query protein fold is built by suitable tracking of the incomplete alignment of the structural template and connection of the alignment gaps. These initial lattice folds are very similar to the structures resulting from standard molecular modeling protocols. Then, a Monte Carlo simulated annealing procedure is used to refine the initial structure. The process is controlled by the model's internal force field and a set of loosely defined restraints that keep the lattice chain in the vicinity of the template conformation. The internal force field consists of several knowledge-based statistical potentials that are enhanced by a proper analysis of multiple sequence alignments. The template restraints are implemented such that the model chain can slide along the template structure or even ignore a substantial fraction of the initial alignment. The resulting lattice models are, in most cases, closer (sometimes much closer) to the target structure than the initial threading-based models. All atom models could easily be built from the lattice chains. The method is illustrated on 12 examples of target/template pairs whose initial threading alignments are of varying quality. Possible applications of the proposed method for use in protein function annotation are briefly discussed. %B Proteins %V 37 %P 592–610 %8 dec %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/10651275