%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 International Journal of Molecular Sciences %D 2019 %T Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields %A Maciej Ciemny %A Aleksandra E. Badaczewska-Dawid %A Monika Pikuzinska %A Andrzej Koliński %A Sebastian Kmiecik %K CABS model MC simulations coarse-grained disordered protein protein structure statistical force fields %X The description of protein disordered states is important for understanding protein folding mechanisms and their functions. In this short review, we briefly describe a simulation approach to modeling protein interactions, which involve disordered peptide partners or intrinsically disordered protein regions, and unfolded states of globular proteins. It is based on the CABS coarse-grained protein model that uses a Monte Carlo (MC) sampling scheme and a knowledge-based statistical force field. We review several case studies showing that description of protein disordered states resulting from CABS simulations is consistent with experimental data. The case studies comprise investigations of protein(-)peptide binding and protein folding processes. The CABS model has been recently made available as the simulation engine of multiscale modeling tools enabling studies of protein(-)peptide docking and protein flexibility. Those tools offer customization of the modeling process, driving the conformational search using distance restraints, reconstruction of selected models to all-atom resolution, and simulation of large protein systems in a reasonable computational time. Therefore, CABS can be combined in integrative modeling pipelines incorporating experimental data and other modeling tools of various resolution. %B International Journal of Molecular Sciences %V 20 %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/30708941 %9 Journal Article %& 606 %R 10.3390/ijms20030606 %0 Book Section %B Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics %D 2019 %T Protein Structure Prediction Using Coarse-Grained Models %A Maciej Blaszczyk %A Dominik Gront %A Sebastian Kmiecik %A Mateusz Kurcinski %A Michal Kolinski %A Maciej Ciemny %A Katarzyna Ziolkowska %A Marta Panek %A Andrzej Koliński %X The knowledge of the three-dimensional structure of proteins is crucial for understanding many important biological processes. Most of the biologically relevant protein systems are too large for classical, atomistic molecular modeling tools. In such cases, coarse-grained (CG) models offer various opportunities for efficient conformational sampling and thus prediction of the three-dimensional structure. A variety of CG models have been proposed, each based on a similar framework consisting of a set of conceptual components such as protein representation, force field, sampling, etc. In this chapter we discuss these components, highlighting ideas which have proven to be the most successful. As CG methods are usually part of multistage procedures, we also describe approaches used for the incorporation of homology data and all-atom reconstruction methods. %B Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics %I Springer International Publishing %P 27–59 %@ 978-3-319-95843-9 %G eng %U https://doi.org/10.1007/978-3-319-95843-9_2 %R 10.1007/978-3-319-95843-9_2 %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 The Journal of Chemical Physics %D 2018 %T Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study %A Maksim Kouza %A Nguyen Truong Co %A Mai Suan Li %A Sebastian Kmiecik %A Andrzej Koliński %A Andrzej Kloczkowski %A Irina A. Buhimschi %X Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite much progress in the understanding of the protein aggregation process, the factors governing fibril formation rates and fibril stability have not been fully understood. Using lattice models, we have shown that the fibril formation time is controlled by the kinetic stability of the fibril state but not by its energy. Having performed all-atom explicit solvent molecular dynamics simulations with the GROMOS43a1 force field for full-length amyloid beta peptides Aβ40;and Aβ42;and truncated peptides, we demonstrated that kinetic stability can be accessed via mechanical stability in such a way that the higher the mechanical stability or the kinetic stability, the faster the fibril formation. This result opens up a new way for predicting fibril formation rates based on mechanical stability that may be easily estimated by steered molecular dynamics. %B The Journal of Chemical Physics %V 148 %P 215106 %G eng %U https://doi.org/10.1063/1.5028575 %R 10.1063/1.5028575 %0 Journal Article %J Drug Discovery Today %D 2018 %T Protein-peptide docking: opportunities and challenges %A Maciej Pawel Ciemny %A Mateusz Kurcinski %A Karol Kamel %A Andrzej Koliński %A Nawsad Alam %A Ora Schueler-Furman %A Sebastian Kmiecik %X Peptides have recently attracted much attention as promising drug candidates. Rational design of peptide-derived therapeutics usually requires structural characterization of the underlying protein-peptide interaction. Given that experimental characterization can be difficult, reliable computational tools are needed. In recent years, a variety of approaches have been developed for 'protein-peptide docking', that is, predicting the structure of the protein-peptide complex, starting from the protein structure and the peptide sequence, including variable degrees of information about the peptide binding site and/or conformation. In this review, we provide an overview of protein-peptide docking methods and outline their capabilities, limitations, and applications in structure-based drug design. Key challenges are also briefly discussed, such as modeling of large-scale conformational changes upon binding, scoring of predicted models, and optimal inclusion of varied types of experimental data and theoretical predictions into an integrative modeling process. %B Drug Discovery Today %V 23 %P 1530-1537 %G eng %U https://www.sciencedirect.com/science/article/pii/S1359644617305937 %N 8 %R 10.1016/j.drudis.2018.05.006 %0 Journal Article %J Briefings in Bioinformatics %D 2018 %T Protein–peptide docking using CABS-dock and contact information %A Maciej Blaszczyk %A Maciej Ciemny %A Andrzej Koliński %A Mateusz Kurcinski %A Sebastian Kmiecik %X CABS-dock is a computational method for protein–peptide molecular docking that does not require predefinition of the binding site. The peptide is treated as fully flexible, while the protein backbone undergoes small fluctuations and, optionally, large-scale rearrangements. Here, we present a specific CABS-dock protocol that enhances the docking procedure using fragmentary information about protein–peptide contacts. The contact information is used to narrow down the search for the binding peptide pose to the proximity of the binding site. We used information on a single-chosen and randomly chosen native protein–peptide contact to validate the protocol on the peptiDB benchmark. The contact information significantly improved CABS-dock performance. The protocol has been made available as a new feature of the CABS-dock web server at http://biocomp.chem.uw.edu.pl/CABSdock %B Briefings in Bioinformatics %P bby080 %G eng %U http://dx.doi.org/10.1093/bib/bby080 %R 10.1093/bib/bby080 %0 Book Section %B Methods in Molecular Biology %D 2017 %T Highly flexible protein-peptide docking using CABS-dock %A Maciej Ciemny %A Mateusz Kurcinski %A Konrad Kozak %A Andrzej Koliński %A Sebastian Kmiecik %X

Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and significant flexibility of a protein receptor. During CABS-dock docking, the peptide folding and binding process is explicitly simulated and no information about the peptide binding site or its structure, is used. This chapter presents a successful CABS-dock use for docking a potentially therapeutic peptide to a protein target. Moreover, simulation contact maps, a new CABS-dock feature, are described and applied to the docking test case. Finally, a tutorial for running CABS-dock from the command line or command line scripts is provided. The CABS-dock web server is available from http://biocomp.chem.uw.edu.pl/CABSdock/

%B Methods in Molecular Biology %V 1561 %P 69-94 %G eng %R 10.1007/978-1-4939-6798-8_6 %0 Journal Article %J BioMedical Engineering OnLine, 16:71 %D 2017 %T Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motif %A Maciej Ciemny %A Mateusz Kurcinski %A Maciej Blaszczyk %A Andrzej Koliński %A Sebastian Kmiecik %X Background. Many protein–protein interactions are mediated by a short linear motif. Usually, amino acid sequences of those motifs are known or can be predicted. It is much harder to experimentally characterize or predict their structure in the bound form. In this work, we test a possibility of using flexible docking of a short linear motif to predict the interaction interface of the EphB4-EphrinB2 complex (a system extensively studied for its significance in tumor progression). Methods. In the modeling, we only use knowledge about the motif sequence and experimental structures of EphB4-EphrinB2 complex partners. The proposed protocol enables efficient modeling of significant conformational changes in the short linear motif fragment during molecular docking simulation. For the docking simulations, we use the CABS-dock method for docking fully flexible peptides to flexible protein receptors (available as a server at http://biocomp.chem.uw.edu.pl/CABSdock/). Based on the docking result, the protein–protein complex is reconstructed and refined. Results. Using this novel protocol, we obtained an accurate EphB4-EphrinB2 interaction model. Conclusions The results show that the CABS-dock method may be useful as the primary docking tool in specific protein–protein docking cases similar to EphB4-EphrinB2 complex—that is, where a short linear motif fragment can be identified. %B BioMedical Engineering OnLine, 16:71 %G eng %U https://biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-017-0362-7 %R 10.1186/s12938-017-0362-7 %0 Journal Article %J BioMedical Engineering OnLine, 16:73 %D 2017 %T A protocol for CABS-dock protein–peptide docking driven by side-chain contact information %A Mateusz Kurcinski %A Maciej Blaszczyk %A Maciej Ciemny %A Andrzej Koliński %A Sebastian Kmiecik %X Background. The characterization of protein–peptide interactions is a challenge for computational molecular docking. Protein–peptide docking tools face at least two major difficulties: (1) efficient sampling of large-scale conformational changes induced by binding and (2) selection of the best models from a large set of predicted structures. In this paper, we merge an efficient sampling technique with external information about side-chain contacts to sample and select the best possible models. Methods. In this paper we test a new protocol that uses information about side-chain contacts in CABS-dock protein–peptide docking. As shown in our recent studies, CABS-dock enables efficient modeling of large-scale conformational changes without knowledge about the binding site. However, the resulting set of binding sites and poses is in many cases highly diverse and difficult to score. Results. As we demonstrate here, information about a single side-chain contact can significantly improve the prediction accuracy. Importantly, the imposed constraints for side-chain contacts are quite soft. Therefore, the developed protocol does not require precise contact information and ensures large-scale peptide flexibility in the broad contact area. Conclusions. The demonstrated protocol provides the extension of the CABS-dock method that can be practically used in the structure prediction of protein–peptide complexes guided by the knowledge of the binding interface. %B BioMedical Engineering OnLine, 16:73 %G eng %U https://biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-017-0363-6 %R 10.1186/s12938-017-0363-6 %0 Conference Proceedings %B Proceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 195-201, arXiv:1605.09269 %D 2016 %T Flexible protein-peptide docking using CABS-dock with knowledge about the binding site %A Mateusz Kurcinski %A Maciej Ciemny %A Maciej Blaszczyk %A Andrzej Koliński %A Sebastian Kmiecik %X Despite considerable efforts, structural prediction of protein-peptide complexes is still a very challenging task, mainly due to two reasons: high flexibility of the peptides and transient character of their interactions with proteins. Recently we have developed an automated web server CABS-dock (http://biocomp.chem.uw.edu.pl/CABSdock), which conducts flexible protein-peptide docking without any knowledge about the binding site. Our method allows for full flexibility of the peptide, whereas the flexibility of the receptor is restricted to near native conformations considering the main chain, and full flexibility of the side chains. Performance of the CABS-dock server was thoroughly tested on a benchmark of 171 test cases, both bound and unbound. Evaluation of the obtained results showed overall good performance of the method, especially that no information of the binding site was used. From unsuccessful experiments we learned that the accuracy of docking might be significantly improved, if only little information of the binding site was considered. In fact, in real-life applications user typically has access to some data indicating the location and/or structure of the binding site. In the current work, we test and demonstrate the performance of the CABS-dock server with two new features. The first one allows to utilize the knowledge about receptor residue(s) constituting the binding site, and the second one allows to enforce the desired secondary structure on the peptide structure. Based on the given example, we observe significant improvement of the docking accuracy in comparison to the default CABS-dock mode. %B Proceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 195-201, arXiv:1605.09269 %G eng %0 Journal Article %J Scientific Reports %D 2016 %T Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction %A Maciej Ciemny %A Aleksander Debinski %A Marta Paczkowska %A Andrzej Koliński %A Mateusz Kurcinski %A Sebastian Kmiecik %X Protein-peptide interactions are often associated with large-scale conformational changes that are difficult to study either by classical molecular modeling or by experiment. Recently, we have developed the CABS-dock method for flexible protein-peptide docking that enables large-scale rearrangements of the protein chain. In this study, we use CABS-dock to investigate the binding of the p53-MDM2 complex, an element of the cell cycle regulation system crucial for anti-cancer drug design. Experimental data suggest that p53-MDM2 binding is affected by significant rearrangements of a lid region - the N-terminal highly flexible MDM2 fragment; however, the details are not clear. The large size of the highly flexible MDM2 fragments makes p53-MDM2 intractable for exhaustive binding dynamics studies using atomistic models. We performed extensive dynamics simulations using the CABS-dock method, including large-scale structural rearrangements of MDM2 flexible regions. Without a priori knowledge of the p53 peptide structure or its binding site, we obtained near-native models of the p53-MDM2 complex. The simulation results match well the experimental data and provide new insights into the possible role of the lid fragment in p53 binding. The presented case study demonstrates that CABS-dock methodology opens up new opportunities for protein-peptide docking with large-scale changes of the protein receptor structure. %B Scientific Reports %V 6 %P 37532 %G eng %0 Conference Proceedings %B Proceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 207-213, arXiv:1605.09266 %D 2016 %T Towards protein-protein docking with significant structural changes using CABS-dock %A Maciej Ciemny %A Mateusz Kurcinski %A Andrzej Koliński %A Sebastian Kmiecik %X The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover, a disruption of hese mechanisms is frequently postulated as a possible cause of diseases such as Alzheimer's or cancer. For many of biologically relevant cases the structure of protein-protein complexes remain unknown. Therefore computational techniques, including molecular docking, have become a valuable part of drug discovery pipelines. Unfortunately, none of the widely used protein-protein docking tools is free from serious limitations. Typically, in docking simulations the protein flexibility is either completely neglected or very limited. Additionally, some knowledge of the approximate location and/or the shape of the active site is also required. Such limitations arise mostly from the enormous number of degrees of freedom of protein-protein systems. In this paper, an efficient computational method for protein-protein docking is proposed and initially tested on a single docking case. The proposed method is based on a two-step procedure. In the first step, CABS-dock web server for protein-peptide docking is used to dock a peptide, which is the appropriate protein fragment responsible for the protein-protein interaction, to the other protein partner. During peptide docking, no knowledge about the binding site, nor the peptide structure, is used and the peptide is allowed to be fully flexible. In the second step, the docked peptide is used in the structural adjustment of protein complex partners. The proposed method allowed us to obtain a high accuracy model, therefore it provides a promising framework for further advances. %B Proceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 207-213, arXiv:1605.09266 %G eng %0 Journal Article %J The Journal of Chemical Physics %D 2015 %T Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models %A Maksim Kouza %A Nguyen Truong Co %A Phuong Hoang Nguyen %A Andrzej Koliński %A Mai Suan Li %X Fibril formation resulting from protein misfoding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accomodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in slowing down fibril elongation in vivo. %B The Journal of Chemical Physics %V 142 %P 145104 %G eng %R http://dx.doi.org/10.1063/1.4917073 %0 Journal Article %J Task Quarterly %D 2014 %T Key Factors Governing Fibril Formation Of Proteins: Insights From Simulations And Experiments %A Nguyen Truong Co %A Man Hoang Viet %A Phan Minh Truong %A Maksim Kouza %A Mai Suan Li %X Fibril formation of proteins and peptides is associated with a large group of major human diseases, including Alzheimer’s disease, prion disorders, amyotrophic lateral sclerosis, type 2 diabetes, etc. Therefore, understanding the key factors that govern this process is of paramount importance. The fibrillogenesis of polypeptide chains depends on their intrinsic properties as well as on the external conditions. In this mini-review we discuss the relationship between fibril formation kinetics and the sequence, aromaticity, hydrophobicity, charge and population of the so called fibril-prone conformation in a monomer state. The higher the population, the faster is the fibril elongation and this dependence may be described by a single exponential function. This observation opens up a new way to understand the fibrillogenesis of bio-molecules at the monomer level. We will also discuss the influence of the environment with focus on the recently observed dual effect of crowders on the aggregation rates of polypeptide chains. %B Task Quarterly %V 18 %P 245–254 %G eng %N 3 %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 International Journal of Molecular Medicine %D 2011 %T Analysis and optimization of interactions between peptides mimicking the GD2 ganglioside and the monoclonal antibody 14G2a %A Irena Horwacik %A Mateusz Kurcinski %A Malgorzata Bzowska %A Aleksandra K. Kowalczyk %A Dominik Czaplicki %A Andrzej Koliński %A Hanna Rokita %K Amino Acid Sequence %K Antibodies %K Binding Sites %K Cell Line %K Gangliosides %K Gangliosides: immunology %K Humans %K Models %K Molecular %K Molecular Mimicry %K Molecular Sequence Data %K Monoclonal %K Monoclonal: chemistry %K Monoclonal: immunology %K Neuroblastoma %K Neuroblastoma: genetics %K Neuroblastoma: immunology %K Peptide Library %K Peptides %K Peptides: chemistry %K Peptides: immunology %K Structure-Activity Relationship %K Tumor %X

Overexpression of the GD2 ganglioside (GD2) is a hallmark of neuroblastoma. The antigen is used in neuroblastoma diagnosis and to target newly developed therapies to cancer cells. Peptide mimetics are novel approaches in the design of antigens for vaccine development. We previously reported the isolation of five GD2-mimicking peptides from the LX-8 phage display library with the monoclonal antibody (mAb) 14G2a. The goal of our current study was to analyze and optimize the binding of the peptide mimetics to the mAb 14G2a. Therefore, we performed further experiments and supported them with molecular modeling to investigate structure-activity relationships that are the basis for the observed mimicry of GD2 by our peptides. Here, we show that the peptides have overlapping binding sites on the mAb, 14G2a and restricted specificity, as they did not crossreact with other ganglioside-specific antibodies tested. In addition we demonstrate that the phage environment was involved in the process of selection of our peptides. The AAEGD sequence taken from the viral major coat protein, p8, and added to the C-termini of the peptides \#65, \#85 and \#94 significantly improved their binding to the mAb, 14G2a. By application of analogs with amino acid substitutions and sequence truncations, we elucidated the structure-activity relationships necessary for the interactions between the 14G2a mAb and the peptide \#94 (RCNPNMEPPRCF). We identified amino acids indispensable for the observed GD2-mimicry by \#94 and confirmed a pivotal role of the disulphide bridge between the cysteine residues of \#94 for binding to the mAb 14G2a. More importantly, we report five new peptides demonstrating a significant improvement of mAb 14G2a binding. The experimental data were supported and expanded with molecular modeling tools. Taken together, the experimental results and the in silico data allowed us to probe in detail the mechanism of the molecular mimicry of GD2 by the peptides. Additionally, we significantly optimized binding of the leading peptide sequence \#94 to the mAb 14G2a. We can conclude that our findings add to the knowledge on factors governing selections of peptide mimetics from phage-display libraries.

%B International Journal of Molecular Medicine %V 28 %P 47–57 %8 jul %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/21455557 %R 10.3892/ijmm.2011.655 %0 Journal Article %J Nucleic Acids Research %D 2011 %T BSDB: the biomolecule stretching database. %A Sikora, Mateusz %A Joanna I. Sulkowska %A Witkowski, Bartlomiej S %A Cieplak, Marek %K Biomechanical Phenomena %K Databases, Protein %K Models, Chemical %K Molecular Dynamics Simulation %K Protein Structure, Secondary %K Proteins %X We describe the Biomolecule Stretching Data Base that has been recently set up at http://www.ifpan.edu.pl/BSDB/. It provides information about mechanostability of proteins. Its core is based on simulations of stretching of 17 134 proteins within a structure-based model. The primary information is about the heights of the maximal force peaks, the force-displacement patterns, and the sequencing of the contact-rupturing events. We also summarize the possible types of the mechanical clamps, i.e. the motifs which are responsible for a protein's resistance to stretching. %B Nucleic Acids Research %V 39 %P D443-50 %8 2011 Jan %G eng %N Database issue %R 10.1093/nar/gkq851 %0 Journal Article %J Biophys J %D 2010 %T Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulations %A G. Arad-Haase %A S.G. Chuartzman %A S. Dagan %A R. Nevo %A Maksim Kouza %A B. K. Mai %A H.T. Nguyen %A M.S. Li %A Z. Reich %X Single-molecule manipulation methods provide a powerful means to study protein transitions. Here we combined single-molecule force spectroscopy and steered molecular-dynamics simulations to study the mechanical properties and unfolding behavior of the small enzyme acylphosphatase (AcP). We find that mechanical unfolding of AcP occurs at relatively low forces in an all-or-none fashion and is decelerated in the presence of a ligand, as observed in solution measurements. The prominent energy barrier for the transition is separated from the native state by a distance that is unusually long for alpha/beta proteins. Unfolding is initiated at the C-terminal strand (beta(T)) that lies at one edge of the beta-sheet of AcP, followed by unraveling of the strand located at the other. The central strand of the sheet and the two helices in the protein unfold last. Ligand binding counteracts unfolding by stabilizing contacts between an arginine residue (Arg-23) and the catalytic loop, as well as with beta(T) of AcP, which renders the force-bearing units of the protein resistant to force. This stabilizing effect may also account for the decelerated unfolding of ligand-bound AcP in the absence of force. %B Biophys J %V 99 %P 238-47 %G eng %0 Journal Article %J Journal of the American Chemical Society %D 2010 %T Untying knots in proteins. %A Joanna I. Sulkowska %A Sułkowski, Piotr %A Szymczak, Piotr %A Cieplak, Marek %K Amino Acids %K Protein Conformation %K Proteins %X A shoelace can be readily untied by pulling its ends rather than its loops. Attempting to untie a native knot in a protein can also succeed or fail depending on where one pulls. However, thermal fluctuations induced by the surrounding water affect conformations stochastically and may add to the uncertainty of the outcome. When the protein is pulled by the termini, the knot can only get tightened, and any attempt at untying results in failure. We show that, by pulling specific amino acids, one may easily retract a terminal segment of the backbone from the knotting loop and untangle the knot. At still other amino acids, the outcome of pulling can go either way. We study the dependence of the untying probability on the way the protein is grasped, the pulling speed, and the temperature. Elucidation of the mechanisms underlying this dependence is critical for a successful experimental realization of protein knot untying. %B Journal of the American Chemical Society %V 132 %P 13954-6 %8 2010 Oct 13 %G eng %N 40 %R 10.1021/ja102441z %0 Journal Article %J PLoS Comput Biol %D 2009 %T Mechanical strength of 17,134 model proteins and cysteine slipknots. %A Sikora, Mateusz %A Joanna I. Sulkowska %A Cieplak, Marek %K Amino Acids %K Cysteine %K elasticity %K Humans %K Models, Molecular %K Molecular Dynamics Simulation %K Protein Folding %K Proteins %K Tensile Strength %X A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17,134 proteins as described by a structure-based model. The proteins selected have no gaps in their structure determination and consist of no more than 250 amino acids. Our previous studies have dealt with 7510 proteins of no more than 150 amino acids. The proteins are ranked according to the strength of the resistance. Most of the predicted top-strength proteins have not yet been studied experimentally. Architectures and folds which are likely to yield large forces are identified. New types of potent force clamps are discovered. They involve disulphide bridges and, in particular, cysteine slipknots. An effective energy parameter of the model is estimated by comparing the theoretical data on characteristic forces to the corresponding experimental values combined with an extrapolation of the theoretical data to the experimental pulling speeds. These studies provide guidance for future experiments on single molecule manipulation and should lead to selection of proteins for applications. A new class of proteins, involving cysteine slipknots, is identified as one that is expected to lead to the strongest force clamps known. This class is characterized through molecular dynamics simulations. %B PLoS Comput Biol %V 5 %P e1000547 %8 2009 Oct %G eng %N 10 %R 10.1371/journal.pcbi.1000547 %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 ACTA PHYSICA POLONICA A %D 2009 %T Tests of the Structure-Based Models of Proteins %A Cieplak, Marek %A Joanna I. Sulkowska %X The structure-based models of proteins are deØned through the condition that their ground state coincides with the native structure of the proteins. There are many variants of such models and they yield different properties. Optimal variants can be selected by making comparisons to experimental data on single-molecule stretching. Here, we discuss the 15 best performing variants and focus on Øne tuning the selection process by adjusting the velocity of stretching to match the experimental conditions. The very best variant is found to correspond to the 10-12 potential in the native contacts with the energies modulated by the Miyazawa{Jernigan statistical potential and variable length parameters. The second best model incorporates the Lennard{Jones potential with uniform amplitudes. We then make a detailed comparison of the two models in which theoretical surveys of stretching properties of 7510 proteins were made previously. %B ACTA PHYSICA POLONICA A %V 115 %G eng %N 2 %& 441 %0 Journal Article %J Proteins %D 2008 %T Predicting the order in which contacts are broken during single molecule protein stretching experiments. %A Joanna I. Sulkowska %A Kloczkowski, Andrzej %A Sen, Taner Z %A Cieplak, Marek %A Jernigan, Robert L %K Green Fluorescent Proteins %K Models, Chemical %K Protein Denaturation %K Proteins %K Tensile Strength %X We combine two methods to enable the prediction of the order in which contacts are broken under external stretching forces in single molecule experiments. These two methods are Gō-like models and elastic network models. The Gō-like models have shown remarkable success in representing many aspects of protein behavior, including the reproduction of experimental data obtained from atomic force microscopy. The simple elastic network models are often used successfully to predict the fluctuations of residues around their mean positions, comparing favorably with the experimentally measured crystallographic B-factors. The behavior of biomolecules under external forces has been demonstrated to depend principally on their elastic properties and the overall shape of their structure. We have studied in detail the muscle protein titin and green fluorescent protein and tested for ten other proteins. First, we stretch the proteins computationally by performing stochastic dynamics simulations with the Gō-like model. We obtain the force-displacement curves and unfolding scenarios of possible mechanical unfolding. We then use the elastic network model to calculate temperature factors (B-factors) and compare the slowest modes of motion for the stretched proteins and compare them with the predicted order of breaking contacts between residues in the Gō-like model. Our results show that a simple Gaussian network model is able to predict contacts that break in the next time stage of stretching. Additionally, we have found that the contact disruption is strictly correlated with the highest force exerted by the backbone on these residues. Our prediction of bond-breaking agrees well with the unfolding scenario obtained with the Gō-like model. We anticipate that this method will be a useful new tool for interpreting stretching experiments. %B Proteins %V 71 %P 45-60 %8 2008 Apr %G eng %N 1 %R 10.1002/prot.21652 %0 Journal Article %J Biophys J %D 2008 %T Selection of optimal variants of Gō-like models of proteins through studies of stretching. %A Joanna I. Sulkowska %A Cieplak, Marek %K Analysis of Variance %K Biomechanical Phenomena %K Models, Molecular %K Protein Conformation %K Protein Folding %K Proteins %K Reproducibility of Results %K Temperature %K Thermodynamics %X The Gō-like models of proteins are constructed based on the knowledge of the native conformation. However, there are many possible choices of a Hamiltonian for which the ground state coincides with the native state. Here, we propose to use experimental data on protein stretching to determine what choices are most adequate physically. This criterion is motivated by the fact that stretching processes usually start with the native structure, in the vicinity of which the Gō-like models should work the best. Our selection procedure is applied to 62 different versions of the Gō model and is based on 28 proteins. We consider different potentials, contact maps, local stiffness energies, and energy scales--uniform and nonuniform. In the latter case, the strength of the nonuniformity was governed either by specificity or by properties related to positioning of the side groups. Among them is the simplest variant: uniform couplings with no i, i + 2 contacts. This choice also leads to good folding properties in most cases. We elucidate relationship between the local stiffness described by a potential which involves local chirality and the one which involves dihedral and bond angles. The latter stiffness improves folding but there is little difference between them when it comes to stretching. %B Biophys J %V 95 %P 3174-91 %8 2008 Oct %G eng %N 7 %R 10.1529/biophysj.107.127233 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2008 %T Stabilizing effect of knots on proteins. %A Joanna I. Sulkowska %A Sulkowski, Piotr %A Szymczak, P %A Cieplak, Marek %K Computer Simulation %K Disulfides %K Hot Temperature %K Humans %K Models, Chemical %K Ornithine Carbamoyltransferase %K Protein Folding %K Protein Structure, Secondary %K Stress, Mechanical %X Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot. %B Proceedings of the National Academy of Sciences of the United States of America %V 105 %P 19714-9 %8 2008 Dec 16 %G eng %N 50 %R 10.1073/pnas.0805468105 %0 Journal Article %J Biophys J %D 2008 %T Stretching to understand proteins - a survey of the protein data bank. %A Joanna I. Sulkowska %A Cieplak, Marek %K Computer Simulation %K Databases, Protein %K elasticity %K Models, Chemical %K Models, Molecular %K Proteins %K Sequence Analysis, Protein %K Stress, Mechanical %K Structure-Activity Relationship %X We make a survey of resistance of 7510 proteins to mechanical stretching at constant speed as studied within a coarse-grained molecular dynamics model. We correlate the maximum force of resistance with the native structure, predict proteins which should be especially strong, and identify the nature of their force clamps. %B Biophys J %V 94 %P 6-13 %8 2008 Jan 1 %G eng %N 1 %R 10.1529/biophysj.107.105973 %0 Journal Article %J Phys Rev Lett %D 2008 %T Tightening of knots in proteins. %A Joanna I. Sulkowska %A Sułkowski, Piotr %A Szymczak, P %A Cieplak, Marek %K Algorithms %K Diffusion %K Models, Molecular %K Protein Conformation %K Solvents %K Stochastic Processes %K Temperature %X We perform theoretical studies of stretching of 20 proteins with knots within a coarse-grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns, whereas in homopolymers they diffuse around and eventually slide off. The waiting times of the jumps are increasingly stochastic as the temperature is raised. Knots typically do not return to their native locations when a protein is released after stretching. %B Phys Rev Lett %V 100 %P 058106 %8 2008 Feb 8 %G eng %N 5 %0 Journal Article %J Journal of Physics: Condensed Matter %D 2007 %T Mechanical stretching of proteins—a theoretical survey of the Protein Data Bank %A Joanna I. Sulkowska %A Cieplak, Marek %X The mechanical stretching of single proteins has been studied experimentally for about 50 proteins, yielding a variety of force patterns and peak forces. Here we perform a theoretical survey of proteins of known native structure and map out the landscape of possible dynamical behaviours under stretching at constant speed. We consider 7510 proteins comprising not more than 150 amino acids and 239 longer proteins. The model used is constructed based on the native geometry. It is solved by methods of molecular dynamics and validated by comparing the theoretical predictions to experimental results. We characterize the distribution of peak forces and investigate correlations with the system size and with the structure classification as characterized by the CATH scheme. Despite the presence of such correlations, proteins with the same CATH index may belong to different classes of dynamical behaviour. We identify proteins with the biggest forces and show that they belong to few topology classes. We determine which protein segments act as mechanical clamps and show that, in most cases, they correspond to long stretches of parallel β-strands, but other mechanisms are also possible. %B Journal of Physics: Condensed Matter %V 19 %G eng %N 283201 %R 10.1088/0953-8984/19/28/283201 %0 Journal Article %J Biophys J %D 2005 %T Folding of the protein domain hbSBD %A Maksim Kouza %A C. Chang %A S. Hayryan %A T. Yu %A Mai Suan Li %A T. Huang %A C. Hu %X The folding of the alpha-helix domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase complex is studied by the circular dichroism technique in absence of urea. Thermal denaturation is used to evaluate various thermodynamic parameters defining the equilibrium unfolding, which is well described by the two-state model with the folding temperature T(F) = 317.8 +/- 1.95 K and the enthalpy change DeltaH(G) = 19.67 +/- 2.67 kcal/mol. The folding is also studied numerically using the off-lattice coarse-grained Go model and the Langevin dynamics. The obtained results, including the population of the native basin, the free-energy landscape as a function of the number of native contacts, and the folding kinetics, also suggest that the hbSBD domain is a two-state folder. These results are consistent with the biological function of hbSBD in branched-chain alpha-ketoacid dehydrogenase. %B Biophys J %V 89 %P 3353-61 %G eng %0 Journal Article %J J Chem Phys %D 2005 %T Thermal unfolding of proteins. %A Cieplak, Marek %A Joanna I. Sulkowska %K Chemistry, Physical %K Computer Simulation %K Connectin %K Kinetics %K Models, Molecular %K Molecular Conformation %K Muscle Proteins %K Protein Conformation %K Protein Denaturation %K Protein Folding %K Protein Kinases %K Protein Structure, Secondary %K Proteins %K Temperature %K Time Factors %X Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature, contacts break at separate time scales and unfolding proceeds approximately in a way reverse to folding. Features in these scenarios agree with experiments and atomic simulations on titin. %B J Chem Phys %V 123 %P 194908 %8 2005 Nov 15 %G eng %N 19 %R 10.1063/1.2121668 %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