1
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Lipska A, Sieradzan AK, Atmaca S, Czaplewski C, Liwo A. Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches. J Phys Chem Lett 2023; 14:9824-9833. [PMID: 37889895 PMCID: PMC10641867 DOI: 10.1021/acs.jpclett.3c01988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
A reliable representation of local interactions is critical for the accuracy of modeling protein structure and dynamics at both the all-atom and coarse-grained levels. The development of local (mainly torsional) potentials was focused on careful parametrization of the predetermined (usually Fourier) formulas rather than on their physics-based derivation. In this Perspective we discuss the state-of-the-art methods for modeling local interactions, including the scale-consistent theory developed in our laboratory, which implies that the coarse-grained torsional potentials inseparably depend on the virtual-bond angles adjacent to a given dihedral and that multitorsional terms should be considered. We extend the treatment to split the residue-based torsional potentials into the site-based regular and improper torsional potentials. These considerations are illustrated with the revised torsional potentials and improper-torsional potentials involving the l-alanine residue and the improper-torsional potential corresponding to serine-residue enantiomerization. Applications of the new approach in coarse-grained modeling and revising all-atom force fields are discussed.
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Affiliation(s)
- Agnieszka
G. Lipska
- Centre
of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit
Union of Universities in Gdańsk, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Adam K. Sieradzan
- Centre
of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit
Union of Universities in Gdańsk, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland
- Faculty
of Chemistry, University of Gdańsk,
Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sümeyye Atmaca
- Kocaeli
University, Institute of Science,
Umuttepe Yerleşkesi, 41001 İzmit/Kocaeli̇, Türkiye
| | - Cezary Czaplewski
- Centre
of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit
Union of Universities in Gdańsk, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland
- Faculty
of Chemistry, University of Gdańsk,
Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam Liwo
- Centre
of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit
Union of Universities in Gdańsk, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland
- Faculty
of Chemistry, University of Gdańsk,
Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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2
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Kryś JD, Gront D. Coarse-grained potential for hydrogen bond interactions. J Mol Graph Model 2023; 124:108507. [PMID: 37295157 DOI: 10.1016/j.jmgm.2023.108507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 06/12/2023]
Abstract
Understanding protein structure and dynamics is crucial for investigating numerous biological processes. This however requires proper description of molecular interactions, most notably hydrogen bonds, which are the driving force behind the folding of protein sequences into working molecules. Due to the multi-body character of this interaction, proper mathematical formulation has been a matter of long debate in the literature. This description becomes even more complex in reduced protein models. In this contribution, we propose a novel hydrogen bond energy function definition that is based only on Cα positions and used for coarse-grained simulations. We show that this new method has the capability to recognize hydrogen bonds with over 80% accuracy and can successfully identify β-sheet in β-amyloid peptide simulations.
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Affiliation(s)
- Justyna D Kryś
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
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3
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Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. J Chem Theory Comput 2023; 19:7112-7135. [PMID: 37788237 DOI: 10.1021/acs.jctc.3c00733] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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Affiliation(s)
- Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Ilias Patmanidis
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Akhil P Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Lucianna H S Santos
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Inserm, CNRS, 06560 Valbonne, France
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita, Okayama 700-8530, Japan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
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4
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Liwo A, Pyrka M, Czaplewski C, Peng X, Niemi AJ. Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach. Biomolecules 2023; 13:941. [PMID: 37371521 DOI: 10.3390/biom13060941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Molecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly efficient. In this study, we investigated the long-term dynamics of the designed left-handed alpha/alpha toroid (PDB: 4YY2), the RBM2 flagellum protein ring from Salmonella (PDB: 6SD5), and the V-type Na+-ATPase rotor in Enterococcus hirae (PDB: 2BL2) using microcanonical and canonical molecular dynamics simulations with the coarse-grained UNRES force field, including a lipid-membrane model, on a millisecond laboratory time scale. Our results demonstrate that rotational motion can occur with zero total angular momentum in the microcanonical regime and that thermal motions can be converted into net rotation in the canonical regime, as previously observed in simulations of smaller cyclic molecules. For 6SD5 and 2BL2, net rotation (with a ratcheting pattern) occurring only about the pivot of the respective system was observed in canonical simulations. The extent and direction of the rotation depended on the initial conditions. This result suggests that rotatory molecular motors can convert thermal oscillations into net rotational motion. The energy from ATP hydrolysis is required probably to set the direction and extent of rotation. Our findings highlight the importance of molecular-motor structures in facilitating movement and transportation within living organisms.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Maciej Pyrka
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland
- Department of Physics and Biophysics, University of Warmia and Mazury, ul. Oczapowskiego 4, 10-719 Olsztyn, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Antti J Niemi
- Nordita, Stockholm University and Uppsala University, Roslagstullsbacken 23, SE-106 91 Stockholm, Sweden
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5
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Li T, Hendrix E, He Y. Simple and Effective Conformational Sampling Strategy for Intrinsically Disordered Proteins Using the UNRES Web Server. J Phys Chem B 2023; 127:2177-2186. [PMID: 36827446 DOI: 10.1021/acs.jpcb.2c08945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Intrinsically disordered proteins (IDPs) contain more charged amino acids than folded proteins, resulting in a lack of hydrophobic core(s) and a tendency to adopt rapidly interconverting structures rather than well-defined structures. The structural heterogeneity of IDPs, encoded by the amino acid sequence, is closely related to their unique roles in biological pathways, which require them to interact with different binding partners. Recently, Robustelli and co-workers have demonstrated that a balanced all-atom force field can be used to sample heterogeneous structures of disordered proteins ( Proc. Natl. Acad. Sci. U.S.A. 2018, 115, E4758-E4766). However, such a solution requires extensive computational resources, such as Anton supercomputers. Here, we propose a simple and effective solution to sample the conformational space of IDPs using a publicly available web server, namely, the UNited-RESidue (UNRES) web server. Our proposed solution requires no investment in computational resources and no prior knowledge of UNRES. UNRES Replica Exchange Molecular Dynamics (REMD) simulations were carried out on a set of eight disordered proteins at temperatures spanning from 270 to 430 K. Utilizing the latest UNRES force field designed for structured proteins, with proper selections of temperatures, we were able to produce comparable results to all-atom force fields as reported in work done by Robustelli and co-workers. In addition, NMR observables and the radius of gyration calculated from UNRES ensembles were directly compared with the experimental data to further evaluate the accuracy of the UNRES model at all temperatures. Our results suggest that carrying out the UNRES simulations at optimal temperatures using the UNRES web server can be a good alternative to sample heterogeneous structures of IDPs.
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Affiliation(s)
- Tongtong Li
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Emily Hendrix
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States.,Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico 87131, United States
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6
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Lipska AG, Sieradzan AK, Czaplewski C, Lipińska AD, Ocetkiewicz KM, Proficz J, Czarnul P, Krawczyk H, Liwo A. Long-time scale simulations of virus-like particles from three human-norovirus strains. J Comput Chem 2023; 44:1470-1483. [PMID: 36799410 DOI: 10.1002/jcc.27087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/29/2023] [Indexed: 02/18/2023]
Abstract
The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that sits in the VLP shell) and the P2 subdomain (that protrudes outside) of the major VP1 protein, this resulting in a correlated wagging motion of the P2 subdomains with respect to the VLP surface. The fluctuations of the P2 subdomain were found to be more pronounced and the P2 domain made a greater angle with the normal to the VLP surface for the GII.2 strain, which could explain the inability of this strain to bind the histo-blood group antigens (HBGAs).
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Affiliation(s)
- Agnieszka G Lipska
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Adam K Sieradzan
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Cezary Czaplewski
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Andrea D Lipińska
- Laboratory of Virus Molecular Biology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Krzysztof M Ocetkiewicz
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Jerzy Proficz
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Paweł Czarnul
- Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Henryk Krawczyk
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Adam Liwo
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
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7
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Sieradzan AK, Sans-Duñó J, Lubecka EA, Czaplewski C, Lipska AG, Leszczyński H, Ocetkiewicz KM, Proficz J, Czarnul P, Krawczyk H, Liwo A. Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins. J Comput Chem 2023; 44:602-625. [PMID: 36378078 DOI: 10.1002/jcc.27026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/19/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022]
Abstract
We report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms to minimize the number of operations and to improve numerical stability, (iv) using OpenMP to parallelize those sections of the code for which distributed-memory parallelization involves unfavorable computing/communication time ratio, and (v) careful memory management to minimize simultaneous access of distant memory sections. The new code enables us to run molecular dynamics simulations of protein systems with size exceeding 100,000 amino-acid residues, reaching over 1 ns/day (1 μs/day in all-atom timescale) with 24 cores for proteins of this size. Parallel performance of the code and comparison of its performance with that of AMBER, GROMACS and MARTINI 3 is presented.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Jordi Sans-Duñó
- Department of Chemistry, University of Lleida, Lleida, Spain
| | - Emilia A Lubecka
- Faculty of Electronics, Telecommunication and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Henryk Leszczyński
- Faculty of Mathematics, Physics and Informatics, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Krzysztof M Ocetkiewicz
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Jerzy Proficz
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Paweł Czarnul
- Faculty of Electronics, Telecommunication and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Henryk Krawczyk
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Faculty of Electronics, Telecommunication and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
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8
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Ślusarz R, Lubecka EA, Czaplewski C, Liwo A. Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions. Front Mol Biosci 2022; 9:1071428. [PMID: 36589235 PMCID: PMC9794589 DOI: 10.3389/fmolb.2022.1071428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
In this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the α+β structures. The scope of applications of the package was extended to data-assisted simulations with restraints from nuclear magnetic resonance (NMR) and chemical crosslink mass-spectroscopy (XL-MS) measurements. NMR restraints can be input in the NMR Exchange Format (NEF), which has become a standard. Ambiguous NMR restraints are handled without expert intervention owing to a specially designed penalty function. The server can be used to run smaller jobs directly or to prepare input data to run larger production jobs by using standalone installations of UNRES.
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Affiliation(s)
- Rafał Ślusarz
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Emilia A. Lubecka
- Faculty of Electronics, Telecommunication and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland,*Correspondence: Adam Liwo,
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9
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Sikorska C, Liwo A. Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery. J Phys Chem B 2022; 126:9493-9505. [PMID: 36367920 PMCID: PMC9706564 DOI: 10.1021/acs.jpcb.2c04610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
By analyzing the Kubo-cluster-cumulant expansion of the potential of mean force of polypeptide chains corresponding to backbone-local interactions averaged over the rotation of the peptide groups about the Cα···Cα virtual bonds, we identified two important kinds of "along-chain" correlations that pertain to extended chain segments bordered by turns (usually the β-strands) and to the folded spring-like segments (usually α-helices), respectively, and are expressed as multitorsional potentials. These terms affect the positioning of structural elements with respect to each other and, consequently, contribute to determining their packing. Additionally, for extended chain segments, the correlation terms contribute to propagating the conformational change at one end to the other end, which is characteristic of allosteric interactions. We confirmed both findings by statistical analysis of the virtual-bond geometry of 77 950 proteins. Augmenting coarse-grained and, possibly, all-atom force fields with these correlation terms could improve their capacity to model protein structure and dynamics.
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Affiliation(s)
- Celina Sikorska
- The
MacDiarmid Institute for Advanced Materials and Nanotechnology, Department
of Physics, The University of Auckland,
Private Bag 92019, Auckland1142, New Zealand
| | - Adam Liwo
- Faculty
of Chemistry, University of Gdańsk,
Fahrenheit Union of Universities in Gdańsk, Wita Stwosza 63, 80-308Gdańsk, Poland,. Phone: +48585235124. Fax: +48585235012
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10
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Lubecka EA, Liwo A. A coarse-grained approach to NMR-data-assisted modeling of protein structures. J Comput Chem 2022; 43:2047-2059. [PMID: 36134668 DOI: 10.1002/jcc.27003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/03/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022]
Abstract
The ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically selects consistent restraints. Hamiltonian replica exchange molecular dynamics was used to carry out the conformational search. The method was tested with both unambiguous and ambiguous restraints producing good-quality models with GDT_TS from 7.4 units higher to 14.4 units lower than those obtained with the CYANA or MELD software for protein-structure determination from NMR data at the all-atom resolution. The method can thus be applied in modeling the structures of flexible proteins, for which extensive conformational search enabled by coarse-graining is more important than high modeling accuracy.
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Affiliation(s)
- Emilia A Lubecka
- Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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11
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Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model. Biomolecules 2022; 12:biom12081140. [PMID: 36009034 PMCID: PMC9406146 DOI: 10.3390/biom12081140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/13/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
The UNited RESidue (UNRES) model of polypeptide chains was applied to study the association of 20 peptides with sizes ranging from 6 to 32 amino-acid residues. Twelve of those were potentially aggregating hexa- or heptapeptides excised from larger proteins, while the remaining eight contained potentially aggregating sequences, functionalized by attaching larger ends rich in charged residues. For 13 peptides, the experimental data of aggregation were used. The remaining seven were synthesized, and their properties were measured in this work. Multiplexed replica-exchange simulations of eight-chain systems were conducted at 12 temperatures from 260 to 370 K at concentrations from 0.421 to 5.78 mM, corresponding to the experimental conditions. The temperature profiles of the fractions of monomers and octamers showed a clear transition corresponding to aggregate dissociation. Low simulated transition temperatures were obtained for the peptides, which did not precipitate after incubation, as well as for the H-GNNQQNY-NH2 prion–protein fragment, which forms small fibrils. A substantial amount of inter-strand β-sheets was found in most of the systems. The results suggest that UNRES simulations can be used to assess peptide aggregation except for glutamine- and asparagine-rich peptides, for which a revision of the UNRES sidechain–sidechain interaction potentials appears necessary.
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12
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Kuncewicz K, Battin C, Węgrzyn K, Sieradzan A, Wardowska A, Sikorska E, Giedrojć I, Smardz P, Pikuła M, Steinberger P, Rodziewicz-Motowidło S, Spodzieja M. Targeting the HVEM protein using a fragment of glycoprotein D to inhibit formation of the BTLA/HVEM complex. Bioorg Chem 2022; 122:105748. [PMID: 35325694 DOI: 10.1016/j.bioorg.2022.105748] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/26/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
Abstract
Cancer immunotherapy using blockade of immune checkpoints is mainly based on monoclonal antibodies. Despite the tremendous success achieved by using those molecules to block immune checkpoint proteins, antibodies possess some weaknesses, which means that there is still a need to search for new compounds as alternatives to antibodies. Many current approaches are focused on use of peptides/peptidomimetics to destroy receptor/ligand interactions. Our studies concern blockade of the BTLA/HVEM complex, which generates an inhibitory effect on the immune response resulting in tolerance to cancer cells. To design inhibitors of such proteins binding we based our work on the amino acid sequence and structure of a ligand of HVEM protein, namely glycoprotein D, which possesses the same binding site on HVEM as BTLA protein. To disrupt the BTLA and HVEM interaction we designed several peptides, all fragments of glycoprotein D, and tested their binding to HVEM using SPR and their ability to inhibit the BTLA/HVEM complex formation using ELISA tests and cellular reporter platforms. That led to identification of two peptides, namely gD(1-36)(K10C-D30C) and gD(1-36)(A12C-L25C), which interact with HVEM and possess blocking capacities. Both peptides are not cytotoxic to human PBMCs, and show stability in human plasma. We also studied the 3D structure of the gD(1-36)(K10C-D30C) peptide using NMR and molecular modeling methods. The obtained data reveal that it possesses an unstructured conformation and binds to HVEM in the same location as gD and BTLA. All these results suggest that peptides based on the binding fragment of gD protein represent promising immunomodulation agents for future cancer immunotherapy.
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Affiliation(s)
| | - Claire Battin
- Medical University of Vienna, Institute of Immunology, Division of Immune Receptors and T cell Activation, 1090 Vienna, Austria
| | - Katarzyna Węgrzyn
- University of Gdańsk, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, 80-307 Gdańsk, Poland
| | - Adam Sieradzan
- University of Gdańsk, Faculty of Chemistry, 80-308 Gdańsk, Poland
| | - Anna Wardowska
- Medical University of Gdańsk, Department of Physiopathology, 80-210 Gdańsk, Poland
| | - Emilia Sikorska
- University of Gdańsk, Faculty of Chemistry, 80-308 Gdańsk, Poland
| | - Irma Giedrojć
- University of Gdańsk, Faculty of Chemistry, 80-308 Gdańsk, Poland
| | - Pamela Smardz
- University of Gdańsk, Faculty of Chemistry, 80-308 Gdańsk, Poland
| | - Michał Pikuła
- Medical University of Gdańsk, Department of Embryology, Laboratory of Tissue Engineering and Regenerative Medicine, 80-210 Gdańsk, Poland
| | - Peter Steinberger
- Medical University of Vienna, Institute of Immunology, Division of Immune Receptors and T cell Activation, 1090 Vienna, Austria
| | | | - Marta Spodzieja
- University of Gdańsk, Faculty of Chemistry, 80-308 Gdańsk, Poland.
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13
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Roterman I, Sieradzan A, Stapor K, Fabian P, Wesołowski P, Konieczny L. On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field. J Mol Graph Model 2022; 114:108166. [PMID: 35325843 DOI: 10.1016/j.jmgm.2022.108166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
During the protein folding process in computer simulations involving the use of a United RESidue (UNRES) force field, an additional module was introduced to represent directly the presence of a polar solvent in water form. This module implements the fuzzy oil drop model (FOD) where the 3D Gauss function expresses the presence of a polar environment which directs the polypeptide chain folding process towards the generation of a centric hydrophobic core. Sample test polypeptide chains of 8 proteins with chain lengths ranging from 37 to 75 aa were simulated in silico using the UNRES (U) package with an implicit solvent model and a built-in module expressing the FOD model (UNRES-FOD-UNRES (U + F) interleaved simulation). The protein structure obtained by both *** simulation schemes, i.e., accordingly***U and U + F, for all the analyzed protein models shows the presence of a hydrophobic core including where it is absent in the native structure. The proposed FOD-M model (M-modified) explaining the source of this phenomenon reveals the need to modify the external field expressing the role of a folding environment. The modification takes into account the influence of other than polar factors present in the folding environment.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College Medyczna 7, 30-688, Kraków, Poland.
| | - Adam Sieradzan
- Faculty of Chemistry, Gdansk University, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Katarzyna Stapor
- Faculty of Automatic, Electronics and Computer Science, Department of Applied Informatics, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
| | - Piotr Fabian
- Faculty of Automatic, Electronics and Computer Science, Department of Algorithmics and Software, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
| | - Patryk Wesołowski
- Faculty of Chemistry, Gdansk University, Wita Stwosza 63, 80-308, Gdańsk, Poland; Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307, Gdańsk, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry - Jagiellonian University - Medical College, Kopernika 7, 31-034, Kraków, Poland.
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14
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2376:399-416. [PMID: 34845623 DOI: 10.1007/978-1-0716-1716-8_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics and its replica-exchange extensions, UNRES has found a variety of applications, including ab initio and database-assisted protein-structure prediction, simulating protein-folding pathways, exploring protein free-energy landscapes, and solving biological problems. This chapter provides a summary of UNRES and a guide for potential users regarding the application of the UNRES package in a variety of research tasks.
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15
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Rojas AV, Maisuradze GG, Scheraga HA, Liwo A. Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field. Methods Mol Biol 2022; 2340:79-104. [PMID: 35167071 DOI: 10.1007/978-1-0716-1546-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation is the cause of many, often lethal, diseases, including the Alzheimer's, Parkinson's, and Huntington's diseases, and familial amyloidosis. Theoretical investigation of the mechanism of this process, including the structures of the oligomeric intermediates which are the most toxic, is difficult because of long time scale of aggregation. Coarse-grained models, which enable us to extend the simulation time scale by three or more orders of magnitude, are, therefore, of great advantage in such studies. In this chapter, we describe the application of the physics-based UNited RESidue (UNRES) force field developed in our laboratory to study protein aggregation, in both free simulations and simulations of aggregation propagation from an existing template (seed), and illustrate it with the examples of Aβ-peptide aggregation and Aβ-peptide-assisted aggregation of the peptides derived from the repeat domains of tau (TauRD).
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Affiliation(s)
- Ana V Rojas
- Schrodinger Inc., 120 West 45th Street New York, New York, 10036, NY, USA
| | - Gia G Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, 14853-1301, NY, USA
| | - Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, 14853-1301, NY, USA
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.
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16
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Liwo A, Czaplewski C, Sieradzan AK, Lipska AG, Samsonov SA, Murarka RK. Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems. Biomolecules 2021; 11:1347. [PMID: 34572559 PMCID: PMC8465211 DOI: 10.3390/biom11091347] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022] Open
Abstract
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink's group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Agnieszka G. Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Sergey A. Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Rajesh K. Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, MP, India;
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17
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Antoniak A, Biskupek I, Bojarski KK, Czaplewski C, Giełdoń A, Kogut M, Kogut MM, Krupa P, Lipska AG, Liwo A, Lubecka EA, Marcisz M, Maszota-Zieleniak M, Samsonov SA, Sieradzan AK, Ślusarz MJ, Ślusarz R, Wesołowski PA, Ziȩba K. Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment. J Mol Graph Model 2021; 108:108008. [PMID: 34419932 DOI: 10.1016/j.jmgm.2021.108008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/31/2022]
Abstract
The UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES-contact group), and (iii) template-assisted (the UNRES-template group). For most of the targets, the contact restraints were derived from the server models top-ranked by the DeepQA method, while the DNCON2 method was used for 11 targets. Our consensus-fragment procedure was used to run template-assisted predictions. Each group also processed the Nuclear Magnetic Resonance (NMR)- and Small Angle X-Ray Scattering (SAXS)-data assisted targets. The average Global Distance Test Total Score (GDT_TS) of the 'Model 1' predictions were 29.17, 39.32, and 56.37 for the UNRES, UNRES-contact, and UNRES-template predictions, respectively, increasing by 0.53, 2.24, and 3.76, respectively, compared to CASP13. It was also found that the GDT_TS of the UNRES models obtained in ab initio mode and in the contact-assisted mode decreases with the square root of chain length, while the exponent in this relationship is 0.20 for the UNRES-template group models and 0.11 for the best performing AlphaFold2 models, which suggests that incorporation of database information, which stems from protein evolution, brings in long-range correlations, thus enabling the correction of force-field inaccuracies.
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Affiliation(s)
- Anna Antoniak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Iga Biskupek
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Krzysztof K Bojarski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Mateusz Kogut
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Małgorzata M Kogut
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, Warsaw, PL-02668, Poland
| | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, 87 Hoegiro, Dongdaemun-gu, 130-722, Seoul, Republic of Korea.
| | - Emilia A Lubecka
- Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Mateusz Marcisz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland; Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307, Gdańsk, Poland
| | | | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Magdalena J Ślusarz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Rafał Ślusarz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Patryk A Wesołowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland; Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307, Gdańsk, Poland
| | - Karolina Ziȩba
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
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18
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Kogut M, Gong Z, Tang C, Liwo A. Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures. J Comput Chem 2021; 42:2054-2067. [PMID: 34402552 DOI: 10.1002/jcc.26736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/09/2021] [Accepted: 08/03/2021] [Indexed: 11/08/2022]
Abstract
Pseudopotentials for the chemical cross-links comprising the glutamic- and aspartic-acid side chains bridged with adipic- (ADH) or pimelic-acid hydrazide (PDH), and the lysine side chains bridged with glutaric (BS2 G) or suberic acid (BS3 ) for coarse-grained cross-link-assisted simulations were determined by canonical molecular dynamics with the Amber14sb force field. The potentials depend on the distance between side-chain ends and on side-chain orientation, this preventing from making cross-link contacts across the globule in simulations. The potentials were implemented in the UNRES coarse-grained force field and their effect on the quality of models was assessed with 11 monomeric and 1 dimeric proteins, using synthetic or experimental cross-link data. Simulations with the new potentials resulted in improvement of the generated models compared to unrestrained simulations in more instances compared to those with the statistical potentials.
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Affiliation(s)
- Mateusz Kogut
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Zhou Gong
- Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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19
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Lubecka EA, Liwo A. ESCASA: Analytical estimation of atomic coordinates from coarse-grained geometry for nuclear-magnetic-resonance-assisted protein structure modeling. I. Backbone and H β protons. J Comput Chem 2021; 42:1579-1589. [PMID: 34048074 DOI: 10.1002/jcc.26695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022]
Abstract
A method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN ) protons, and the side-chain Hβ protons, given the Cα -trace, have been derived and parameterized, by using the interproton distances calculated from a set of 140 high-resolution non-homologous protein structures. The mean standard deviation over all types of proton pairs in the set was 0.44 Å after fitting. Validation against a set of 41 proteins with NMR-determined structures, which were not considered in parameterization, resulted in average standard deviation from average proton-proton distances of the NMR-determined structures of 0.25 Å, compared to 0.21 Å obtained with the PULCHRA all-atom-chain reconstruction algorithm and to the 0.12 Å standard deviation of the average-structure proton-proton distance of NMR-determined ensembles. The formulas provide analytical forces and can, therefore, be used in coarse-grained molecular dynamics.
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Affiliation(s)
- Emilia A Lubecka
- Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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20
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Giulini M, Rigoli M, Mattiotti G, Menichetti R, Tarenzi T, Fiorentini R, Potestio R. From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules. Front Mol Biosci 2021; 8:676976. [PMID: 34164432 PMCID: PMC8215203 DOI: 10.3389/fmolb.2021.676976] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/06/2021] [Indexed: 12/18/2022] Open
Abstract
The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.
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Affiliation(s)
- Marco Giulini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Marta Rigoli
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Giovanni Mattiotti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Roberto Menichetti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Thomas Tarenzi
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaele Fiorentini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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21
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Postic G, Janel N, Moroy G. Representations of protein structure for exploring the conformational space: A speed-accuracy trade-off. Comput Struct Biotechnol J 2021; 19:2618-2625. [PMID: 34025948 PMCID: PMC8120936 DOI: 10.1016/j.csbj.2021.04.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/25/2022] Open
Abstract
We compare ten structural representations, either atomistic or coarse-grained. Thus, ten distance-dependent statistical potentials of mean force (PMF) were built. The Cβ-only and Cα + Cβ representations provide the best speed–accuracy trade-off. Including glycines through Cα, in a Cβ-only representation, yields a higher accuracy. We generalize the conclusions to the total information gain (TIG) scoring function.
The recent breakthrough in the field of protein structure prediction shows the relevance of using knowledge-based based scoring functions in combination with a low-resolution 3D representation of protein macromolecules. The choice of not using all atoms is barely supported by any data in the literature, and is mostly motivated by empirical and practical reasons, such as the computational cost of assessing the numerous folds of the protein conformational space. Here, we present a comprehensive study, carried on a large and balanced benchmark of predicted protein structures, to see how different types of structural representations rank in either accuracy or calculation speed, and which ones offer the best compromise between these two criteria. We tested ten representations, including low-resolution, high-resolution, and coarse-grained approaches. We also investigated the generalization of the findings to other formalisms than the widely-used “potential of mean force” (PMF) method. Thus, we observed that representing protein structures by their β carbons—combined or not with Cα—provides the best speed–accuracy trade-off, when using a “total information gain” scoring function. For statistical PMFs, using MARTINI backbone and side-chains beads is the best option. Finally, we also demonstrated the necessity of training the reference state on all atom types, and of including the Cα atoms of glycine residues, in a Cβ-based representation.
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Affiliation(s)
- Guillaume Postic
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013 Paris, France
- Corresponding author.
| | - Nathalie Janel
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Gautier Moroy
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013 Paris, France
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22
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Stevens AO, He Y. Residue-Level Contact Reveals Modular Domain Interactions of PICK1 Are Driven by Both Electrostatic and Hydrophobic Forces. Front Mol Biosci 2021; 7:616135. [PMID: 33585564 PMCID: PMC7873044 DOI: 10.3389/fmolb.2020.616135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022] Open
Abstract
PICK1 is a multi-domain scaffolding protein that is uniquely comprised of both a PDZ domain and a BAR domain. While previous experiments have shown that the PDZ domain and the linker positively regulate the BAR domain and the C-terminus negatively regulates the BAR domain, the details of internal regulation mechanisms are unknown. Molecular dynamics (MD) simulations have been proven to be a useful tool in revealing the intramolecular interactions at atomic-level resolution. PICK1 performs its biological functions in a dimeric form which is extremely computationally demanding to simulate with an all-atom force field. Here, we use coarse-grained MD simulations to expose the key residues and driving forces in the internal regulations of PICK1. While the PDZ and BAR domains do not form a stable complex, our simulations show the PDZ domain preferentially interacting with the concave surface of the BAR domain over other BAR domain regions. Furthermore, our simulations show that the short helix in the linker region can form interactions with the PDZ domain. Our results reveal that the surface of the βB-βC loop, βC strand, and αA-βD loop of the PDZ domain can form a group of hydrophobic interactions surrounding the linker helix. These interactions are driven by hydrophobic forces. In contrast, our simulations reveal a very dynamic C-terminus that most often resides on the convex surface of the BAR domain rather than the previously suspected concave surface. These interactions are driven by a combination of electrostatic and hydrophobic interactions.
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Affiliation(s)
- Amy O Stevens
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM, United States
| | - Yi He
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM, United States
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23
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Sevink GJA, Liwo JA, Asinari P, MacKernan D, Milano G, Pagonabarraga I. Unfolding the prospects of computational (bio)materials modeling. J Chem Phys 2020; 153:100901. [PMID: 32933271 DOI: 10.1063/5.0019773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this perspective communication, we briefly sketch the current state of computational (bio)material research and discuss possible solutions for the four challenges that have been increasingly identified within this community: (i) the desire to develop a unified framework for testing the consistency of implementation and physical accuracy for newly developed methodologies, (ii) the selection of a standard format that can deal with the diversity of simulation data and at the same time simplifies data storage, data exchange, and data reproduction, (iii) how to deal with the generation, storage, and analysis of massive data, and (iv) the benefits of efficient "core" engines. Expressed viewpoints are the result of discussions between computational stakeholders during a Lorentz center workshop with the prosaic title Workshop on Multi-scale Modeling and are aimed at (i) improving validation, reporting and reproducibility of computational results, (ii) improving data migration between simulation packages and with analysis tools, (iii) popularizing the use of coarse-grained and multi-scale computational tools among non-experts and opening up these modern computational developments to an extended user community.
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Affiliation(s)
- G J Agur Sevink
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Jozef Adam Liwo
- Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Pietro Asinari
- Department of Energy, Politecnico di Torino, Corso Duca degli Abruzzi, 24, 10129 Turin, Italy
| | - Donal MacKernan
- UCD School of Physics, University College Dublin, Dublin 4, Ireland
| | - Giuseppe Milano
- Theoretical Physical Chemistry, Organic Materials Modeling, Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan Yonezawa, Yamagata-ken 992-8510, Japan
| | - Ignacio Pagonabarraga
- CECAM Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne (EPFL), Batochime, Avenue Forel 2, Lausanne CH-1015, Switzerland
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24
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Chrabąszczewska M, Sieradzan AK, Rodziewicz-Motowidło S, Grubb A, Dobson CM, Kumita JR, Kozak M. Structural Characterization of Covalently Stabilized Human Cystatin C Oligomers. Int J Mol Sci 2020; 21:ijms21165860. [PMID: 32824145 PMCID: PMC7461555 DOI: 10.3390/ijms21165860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022] Open
Abstract
Human cystatin C (HCC), a cysteine-protease inhibitor, exists as a folded monomer under physiological conditions but has the ability to self-assemble via domain swapping into multimeric states, including oligomers with a doughnut-like structure. The structure of the monomeric HCC has been solved by X-ray crystallography, and a covalently linked version of HCC (stab-1 HCC) is able to form stable oligomeric species containing 10-12 monomeric subunits. We have performed molecular modeling, and in conjunction with experimental parameters obtained from atomic force microscopy (AFM), transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) measurements, we observe that the structures are essentially flat, with a height of about 2 nm, and the distance between the outer edge of the ring and the edge of the central cavity is ~5.1 nm. These dimensions correspond to the height and diameter of one stab-1 HCC subunit and we present a dodecamer model for stabilized cystatin C oligomers using molecular dynamics simulations and experimentally measured parameters. Given that oligomeric species in protein aggregation reactions are often transient and very highly heterogeneous, the structural information presented here on these isolated stab-1 HCC oligomers may be useful to further explore the physiological relevance of different structural species of cystatin C in relation to protein misfolding disease.
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Affiliation(s)
- Magdalena Chrabąszczewska
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland;
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (A.K.S.); (S.R.-M.)
| | | | - Anders Grubb
- Department of Clinical Chemistry, Lund University Hospital, S-22185 Lund, Sweden;
| | - Christopher M. Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK;
| | - Janet R. Kumita
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK;
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
- Correspondence: (J.R.K.); (M.K.)
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland;
- Correspondence: (J.R.K.); (M.K.)
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25
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Liwo A, Czaplewski C, Sieradzan AK, Lubecka EA, Lipska AG, Golon Ł, Karczyńska A, Krupa P, Mozolewska MA, Makowski M, Ganzynkowicz R, Giełdoń A, Maciejczyk M. Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:73-122. [PMID: 32145953 DOI: 10.1016/bs.pmbts.2019.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this chapter the scale-consistent approach to the derivation of coarse-grained force fields developed in our laboratory is presented, in which the effective energy function originates from the potential of mean force of the system under consideration and embeds atomistically detailed interactions in the resulting energy terms through use of Kubo's cluster-cumulant expansion, appropriate selection of the major degrees of freedom to be averaged out in the derivation of analytical approximations to the energy terms, and appropriate expression of the interaction energies at the all-atom level in these degrees of freedom. Our approach enables the developers to find correct functional forms of the effective coarse-grained energy terms, without having to import them from all-atom force fields or deriving them on a heuristic basis. In particular, the energy terms derived in such a way exhibit correct dependence on coarse-grained geometry, in particular on site orientation. Moreover, analytical formulas for the multibody (correlation) terms, which appear to be crucial for coarse-grained modeling of many of the regular structures such as, e.g., protein α-helices and β-sheets, can be derived in a systematic way. Implementation of the developed theory to the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules, which consists of the UNRES (for proteins), NARES-2P (for nucleic acids), and SUGRES-1P (for polysaccharides) components, and is being developed in our laboratory is described. Successful applications of UNICORN to the prediction of protein structure, simulating the folding and stability of proteins and nucleic acids, and solving biological problems are discussed.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea.
| | | | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Emilia A Lubecka
- Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Gdańsk, Poland
| | | | - Łukasz Golon
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | | | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | | | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Maciej Maciejczyk
- Department of Physics and Biophysics, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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26
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Karczyńska AS, Ziȩba K, Uciechowska U, Mozolewska MA, Krupa P, Lubecka EA, Lipska AG, Sikorska C, Samsonov SA, Sieradzan AK, Giełdoń A, Liwo A, Ślusarz R, Ślusarz M, Lee J, Joo K, Czaplewski C. Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13. J Chem Inf Model 2020; 60:1844-1864. [PMID: 31999919 PMCID: PMC7588044 DOI: 10.1021/acs.jcim.9b00864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The method for protein-structure
prediction, which combines the
physics-based coarse-grained UNRES force field with knowledge-based
modeling, has been developed further and tested in the 13th Community
Wide Experiment on the Critical Assessment of Techniques for Protein
Structure Prediction (CASP13). The method implements restraints from
the consensus fragments common to server models. In this work, the
server models to derive fragments have been chosen on the basis of
quality assessment; a fully automatic fragment-selection procedure
has been introduced, and Dynamic Fragment Assembly pseudopotentials
have been fully implemented. The Global Distance Test Score (GDT_TS),
averaged over our “Model 1” predictions, increased by
over 10 units with respect to CASP12 for the free-modeling category
to reach 40.82. Our “Model 1” predictions ranked 20
and 14 for all and free-modeling targets, respectively (upper 20.2%
and 14.3% of all models submitted to CASP13 in these categories, respectively),
compared to 27 (upper 21.1%) and 24 (upper 18.9%) in CASP12, respectively.
For oligomeric targets, the Interface Patch Similarity (IPS) and Interface
Contact Similarity (ICS) averaged over our best oligomer models increased
from 0.28 to 0.36 and from 12.4 to 17.8, respectively, from CASP12
to CASP13, and top-ranking models of 2 targets (H0968 and T0997o)
were obtained (none in CASP12). The improvement of our method in CASP13
over CASP12 was ascribed to the combined effect of the overall enhancement
of server-model quality, our success in selecting server models and
fragments to derive restraints, and improvements of the restraint
and potential-energy functions.
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Affiliation(s)
| | - Karolina Ziȩba
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Urszula Uciechowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Magdalena A Mozolewska
- Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, Warsaw PL-02668, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, Warsaw PL-02668, Poland
| | - Emilia A Lubecka
- Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Wita Stwosza 57, Gdańsk 80-308, Poland
| | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Celina Sikorska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.,School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.,School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Rafał Ślusarz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Magdalena Ślusarz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Jooyoung Lee
- School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Keehyoung Joo
- Center for Advanced Computation, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
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27
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Liwo A, Czaplewski C. Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins. J Chem Phys 2020; 152:054902. [DOI: 10.1063/1.5138991] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
- School of Computational Sciences, Korea Institute for Advanced Study, 87 Hoegiro, Dongdaemun-gu, 130-722 Seoul, South Korea
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
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28
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Fajardo JE, Shrestha R, Gil N, Belsom A, Crivelli SN, Czaplewski C, Fidelis K, Grudinin S, Karasikov M, Karczyńska AS, Kryshtafovych A, Leitner A, Liwo A, Lubecka EA, Monastyrskyy B, Pagès G, Rappsilber J, Sieradzan AK, Sikorska C, Trabjerg E, Fiser A. Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. Proteins 2019; 87:1283-1297. [PMID: 31569265 PMCID: PMC6851497 DOI: 10.1002/prot.25816] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/08/2019] [Accepted: 09/13/2019] [Indexed: 12/22/2022]
Abstract
With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest-to-date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.
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Affiliation(s)
- J. Eduardo Fajardo
- Department of Systems and Computational Biology, and Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Rojan Shrestha
- Department of Systems and Computational Biology, and Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Nelson Gil
- Department of Systems and Computational Biology, and Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Adam Belsom
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Silvia N. Crivelli
- Department of Computer Science, UC Davis, One Shields Ave., Davis, CA 95616
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Krzysztof Fidelis
- Genome Center, University of California, Davis, 451 Health Sciences Dr., Davis CA 95616-8816, USA
| | - Sergei Grudinin
- Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP LJK, 38000 Grenoble, France
| | - Mikhail Karasikov
- Center for Energy Systems, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
- Moscow Institute of Physics and Technology, Moscow, 141701, Russia
- Department of Computer Science, ETH Zurich, Zurich, 8092, Switzerland
| | | | - Andriy Kryshtafovych
- Genome Center, University of California, Davis, 451 Health Sciences Dr., Davis CA 95616-8816, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
- School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Emilia A. Lubecka
- Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Wita Stwosza 57, 80-308 Gdańsk, Poland
| | - Bohdan Monastyrskyy
- Genome Center, University of California, Davis, 451 Health Sciences Dr., Davis CA 95616-8816, USA
| | - Guillaume Pagès
- Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP LJK, 38000 Grenoble, France
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Celina Sikorska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Esben Trabjerg
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Andras Fiser
- Department of Systems and Computational Biology, and Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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29
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Jin L, Tan YL, Wu Y, Wang X, Shi YZ, Tan ZJ. Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway. RNA (NEW YORK, N.Y.) 2019; 25:1532-1548. [PMID: 31391217 PMCID: PMC6795135 DOI: 10.1261/rna.071662.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/02/2019] [Indexed: 05/08/2023]
Abstract
RNA kissing complexes are essential for genomic RNA dimerization and regulation of gene expression, and their structures and stability are critical to their biological functions. In this work, we used our previously developed coarse-grained model with an implicit structure-based electrostatic potential to predict three-dimensional (3D) structures and stability of RNA kissing complexes in salt solutions. For extensive RNA kissing complexes, our model shows great reliability in predicting 3D structures from their sequences, and our additional predictions indicate that the model can capture the dependence of 3D structures of RNA kissing complexes on monovalent/divalent ion concentrations. Moreover, the comparisons with extensive experimental data show that the model can make reliable predictions on the stability for various RNA kissing complexes over wide ranges of monovalent/divalent ion concentrations. Notably, for RNA kissing complexes, our further analyses show the important contribution of coaxial stacking to the 3D structures and stronger stability than the corresponding kissing-interface duplexes at high salts. Furthermore, our comprehensive analyses for RNA kissing complexes reveal that the thermally folding pathway for a complex sequence is mainly determined by the relative stability of two possible folded states of kissing complex and extended duplex, which can be significantly modulated by its sequence.
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Affiliation(s)
- Lei Jin
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Lan Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yao Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xunxun Wang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan 430073, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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30
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Lubecka EA, Karczyńska AS, Lipska AG, Sieradzan AK, Ziȩba K, Sikorska C, Uciechowska U, Samsonov SA, Krupa P, Mozolewska MA, Golon Ł, Giełdoń A, Czaplewski C, Ślusarz R, Ślusarz M, Crivelli SN, Liwo A. Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment. J Mol Graph Model 2019; 92:154-166. [PMID: 31376733 DOI: 10.1016/j.jmgm.2019.07.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/20/2019] [Accepted: 07/23/2019] [Indexed: 01/17/2023]
Abstract
The recent NEWCT-9P version of the coarse-grained UNRES force field for proteins, with scale-consistent formulas for the local and correlation terms, has been tested in the CASP13 experiment of the blind-prediction of protein structure, in the ab initio, contact-assisted, and data-assisted modes. Significant improvement of the performance has been observed with respect to the CASP11 and CASP12 experiments (by over 10 GDT_TS units for the ab initio mode predictions and by over 15 GDT_TS units for the contact-assisted prediction, respectively), which is a result of introducing scale-consistent terms and improved handling of contact-distance restraints. As in previous CASP exercises, UNRES ranked higher in the free modeling category than in the general category that included template based modeling targets. Use of distance restraints from the predicted contacts, albeit many of them were wrong, resulted in the increase of GDT_TS by over 8 units on average and introducing sparse restraints from small-angle X-ray/neutron scattering and chemical cross-link-mass-spectrometry experiments, and ambiguous restraints from nuclear magnetic resonance experiments has also improved the predictions by 8.6, 9.7, and 10.7 GDT_TS units on average, respectively.
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Affiliation(s)
- Emilia A Lubecka
- Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Wita Stwosza 57, 80-308, Gdańsk, Poland; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | | | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Karolina Ziȩba
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Celina Sikorska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Urszula Uciechowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, Warsaw, PL, 02668, Poland
| | - Magdalena A Mozolewska
- Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, Warsaw, 01-248, Poland
| | - Łukasz Golon
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Rafał Ślusarz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Magdalena Ślusarz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Silvia N Crivelli
- Department of Computer Science, UC Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, 130-722, Seoul, Republic of Korea.
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31
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Sieradzan AK, Bogunia M, Mech P, Ganzynkowicz R, Giełdoń A, Liwo A, Makowski M. Introduction of Phosphorylated Residues into the UNRES Coarse-Grained Model: Toward Modeling of Signaling Processes. J Phys Chem B 2019; 123:5721-5729. [PMID: 31194908 DOI: 10.1021/acs.jpcb.9b03799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Phosphorylated proteins take part in many signaling pathways and play a key role in homeostasis regulation. The all-atom force fields enable us to study the systems containing phosphorylated proteins, but they are limited to short time scales. In this paper, we report the extension of the physics-based coarse-grained UNRES force field to treat systems with phosphorylated amino-acid residues. To derive the respective potentials, appropriate physics-based analytical expressions were fitted to the potentials of mean force of systems modeling phosphorylated amino-acid residues computed in our previous work and implemented in UNRES. The extended UNRES performed well in ab initio simulations of two miniproteins containing phosphorylated residues, strongly suggesting that realistic large-scale simulations of processes involving phosphorylated proteins, especially signaling processes, are now possible.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Małgorzata Bogunia
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Paulina Mech
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Robert Ganzynkowicz
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Artur Giełdoń
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Adam Liwo
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Mariusz Makowski
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
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32
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Lubecka EA, Liwo A. Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints. J Comput Chem 2019; 40:2164-2178. [PMID: 31037754 DOI: 10.1002/jcc.25847] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/29/2019] [Accepted: 04/14/2019] [Indexed: 12/26/2022]
Abstract
Contact-assisted simulations, the contacts being predicted or determined experimentally, have become very important in the determination of the structures of proteins and other biological macromolecules. In this work, the effect of contact-distance restraints on the simulated structures was investigated with the use of multiplexed replica exchange simulations with the coarse-grained UNRES force field. A modified bounded flat-bottom restraint function that does not generate a gradient when a restraint cannot be satisfied was implemented. Calculations were run with (i) a set of four small proteins, with contact restraints derived from experimental structures, and (ii) selected CASP11 and CASP12 targets, with restraints as used at prediction time. The bounded penalty function largely omitted false contacts, which were usually inconsistent. It was found that at least 20% of correct contacts must be present in the restraint set to improve model quality with respect to unrestrained simulations. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Emilia A Lubecka
- Institute of Informatics, Faculty of Mathematics, Physics and Informatics, University of Gdańsk, Wita Stwosza 57, 80-308 Gdańsk, Poland.,Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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33
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Liwo A, Sieradzan AK, Lipska AG, Czaplewski C, Joung I, Żmudzińska W, Hałabis A, Ołdziej S. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation. J Chem Phys 2019; 150:155104. [PMID: 31005069 DOI: 10.1063/1.5093015] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The general theory of the construction of scale-consistent energy terms in the coarse-grained force fields presented in Paper I of this series has been applied to the revision of the UNRES force field for physics-based simulations of proteins. The potentials of mean force corresponding to backbone-local and backbone-correlation energy terms were calculated from the ab initio energy surfaces of terminally blocked glycine, alanine, and proline, and the respective analytical expressions, derived by using the scale-consistent formalism, were fitted to them. The parameters of all these potentials depend on single-residue types, thus reducing their number and preventing over-fitting. The UNRES force field with the revised backbone-local and backbone-correlation terms was calibrated with a set of four small proteins with basic folds: tryptophan cage variant (TRP1; α), Full Sequence Design (FSD; α + β), villin headpiece (villin; α), and a truncated FBP-28 WW-domain variant (2MWD; β) (the NEWCT-4P force field) and, subsequently, with an enhanced set of 9 proteins composed of TRP1, FSD, villin, 1BDC (α), 2I18 (α), 1QHK (α + β), 2N9L (α + β), 1E0L (β), and 2LX7 (β) (the NEWCT-9P force field). The NEWCT-9P force field performed better than NEWCT-4P in a blind-prediction-like test with a set of 26 proteins not used in calibration and outperformed, in a test with 76 proteins, the most advanced OPT-WTFSA-2 version of UNRES with former backbone-local and backbone-correlation terms that contained more energy terms and more optimizable parameters. The NEWCT-9P force field reproduced the bimodal distribution of backbone-virtual-bond angles in the simulated structures, as observed in experimental protein structures.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - InSuk Joung
- School of Computational Sciences, Korea Institute for Advanced Study, 87 Hoegiro, Dongdaemun-gu, 130-722 Seoul, South Korea
| | - Wioletta Żmudzińska
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307 Gdańsk, Poland
| | - Anna Hałabis
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307 Gdańsk, Poland
| | - Stanisław Ołdziej
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307 Gdańsk, Poland
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Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope. Methods Mol Biol 2019. [PMID: 30945217 DOI: 10.1007/978-1-4939-9161-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The secondary structure of proteins results from both local and long-range interactions, the latter being primarily backbone hydrogen bonding. In this chapter, based on our recent work, we suggest that the striking regularity of secondary structure can be described, in a semi-analytical manner, in terms of Kubo cluster cumulants (corresponding to the expansion of the protein's potential of mean force) that originate from the coupling between the backbone-local and backbone-electrostatic interactions. This finding is illustrated by the analysis of the Protein Data Bank statistics. Examples demonstrating the importance of the coupling terms in coarse-grained treatment of proteins are also presented.
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35
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Jin L, Shi YZ, Feng CJ, Tan YL, Tan ZJ. Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions. Biophys J 2018; 115:1403-1416. [PMID: 30236782 DOI: 10.1016/j.bpj.2018.08.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/10/2018] [Accepted: 08/24/2018] [Indexed: 11/16/2022] Open
Abstract
Double-stranded (ds) RNAs play essential roles in many processes of cell metabolism. The knowledge of three-dimensional (3D) structure, stability, and flexibility of dsRNAs in salt solutions is important for understanding their biological functions. In this work, we further developed our previously proposed coarse-grained model to predict 3D structure, stability, and flexibility for dsRNAs in monovalent and divalent ion solutions through involving an implicit structure-based electrostatic potential. The model can make reliable predictions for 3D structures of extensive dsRNAs with/without bulge/internal loops from their sequences, and the involvement of the structure-based electrostatic potential and corresponding ion condition can improve the predictions for 3D structures of dsRNAs in ion solutions. Furthermore, the model can make good predictions for thermal stability for extensive dsRNAs over the wide range of monovalent/divalent ion concentrations, and our analyses show that the thermally unfolding pathway of dsRNA is generally dependent on its length as well as its sequence. In addition, the model was employed to examine the salt-dependent flexibility of a dsRNA helix, and the calculated salt-dependent persistence lengths are in good accordance with experiments.
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Affiliation(s)
- Lei Jin
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China
| | - Chen-Jie Feng
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Lan Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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36
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Sieradzan AK, Golon Ł, Liwo A. Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing. Phys Chem Chem Phys 2018; 20:19656-19663. [PMID: 30014063 DOI: 10.1039/c8cp03018a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A physics-based method for the prediction of the structures of nucleic acids, which is based on the physics-based 2-bead NARES-2P model of polynucleotides and global-optimization Conformational Space Annealing (CSA) algorithm has been proposed. The target structure is sought as the global-energy-minimum structure, which ignores the entropy component of the free energy but spares expensive multicanonical simulations necessary to find the conformational ensemble with the lowest free energy. The CSA algorithm has been modified to optimize its performance when treating both single and multi-chain nucleic acids. It was shown that the method finds the native fold for simple RNA molecules and DNA duplexes and with limited distance restraints, which can easily be obtained from the secondary-structure-prediction servers, complex RNA folds can be treated with using moderate computer resources.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland.
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37
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Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets. J Mol Graph Model 2018; 83:92-99. [DOI: 10.1016/j.jmgm.2018.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 05/18/2018] [Accepted: 05/20/2018] [Indexed: 11/22/2022]
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38
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Czaplewski C, Karczyńska A, Sieradzan AK, Liwo A. UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics. Nucleic Acids Res 2018; 46:W304-W309. [PMID: 29718313 PMCID: PMC6031057 DOI: 10.1093/nar/gky328] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/12/2018] [Accepted: 04/18/2018] [Indexed: 12/24/2022] Open
Abstract
A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.
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Affiliation(s)
- Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Agnieszka Karczyńska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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39
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Karczyńska AS, Mozolewska MA, Krupa P, Giełdoń A, Liwo A, Czaplewski C. Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information. Proteins 2017; 86 Suppl 1:228-239. [PMID: 29134679 DOI: 10.1002/prot.25421] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 11/09/2022]
Abstract
A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment. Major improvement of the GDT_TS was obtained for 2 targets, minor improvement for other 2 while, for 6 target GDT_TS deteriorated compared with that calculated for predictions without the SAXS data, partly because of assuming a wrong multimeric state (for Ts866) or because the crystal conformation was more compact than the solution conformation (for Ts942). Particularly good results were obtained for Ts909, in which use of SAXS data resulted in the selection of a correctly packed trimer and, subsequently, increased the GDT_TS of monomer prediction. It was found that running simulations with correct oligomeric state is essential for the success in SAXS-data-assisted prediction.
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Affiliation(s)
| | - Magdalena A Mozolewska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.,Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, Warsaw, 01-248, Poland
| | - Paweł Krupa
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.,Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, Warsaw, PL-02668, Poland
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.,School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul, 130-722, Republic of Korea
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland
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40
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Lubecka EA, Liwo A. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O1→4-bonded polyglucose chains. J Chem Phys 2017; 147:115101. [DOI: 10.1063/1.4994130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Emilia A. Lubecka
- Institute of Informatics, University of Gdańsk, Wita Stwosza 57, 80-308 Gdańsk, Poland
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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41
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Krupa P, Hałabis A, Żmudzińska W, Ołdziej S, Scheraga HA, Liwo A. Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J Chem Inf Model 2017; 57:2364-2377. [DOI: 10.1021/acs.jcim.7b00254] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Paweł Krupa
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, PL-02668 Warsaw, Poland
| | - Anna Hałabis
- Laboratory of Biopolymer
Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Wioletta Żmudzińska
- Laboratory of Biopolymer
Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Stanisław Ołdziej
- Laboratory of Biopolymer
Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
- School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
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