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Leśniewski M, Pyrka M, Czaplewski C, Co NT, Jiang Y, Gong Z, Tang C, Liwo A. Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures. J Chem Inf Model 2024; 64:1377-1393. [PMID: 38345917 PMCID: PMC10900291 DOI: 10.1021/acs.jcim.3c01890] [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: 11/24/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
Abstract
The influence of distance restraints from chemical cross-link mass spectroscopy (XL-MS) on the quality of protein structures modeled with the coarse-grained UNRES force field was assessed by using a protocol based on multiplexed replica exchange molecular dynamics, in which both simulated and experimental cross-link restraints were employed, for 23 small proteins. Six cross-links with upper distance boundaries from 4 Å to 12 Å (azido benzoic acid succinimide (ABAS), triazidotriazine (TATA), succinimidyldiazirine (SDA), disuccinimidyl adipate (DSA), disuccinimidyl glutarate (DSG), and disuccinimidyl suberate (BS3)) and two types of restraining potentials ((i) simple flat-bottom Lorentz-like potentials dependent on side chain distance (all cross-links) and (ii) distance- and orientation-dependent potentials determined based on molecular dynamics simulations of model systems (DSA, DSG, BS3, and SDA)) were considered. The Lorentz-like potentials with properly set parameters were found to produce a greater number of higher-quality models compared to unrestrained simulations than the MD-based potentials, because the latter can force too long distances between side chains. Therefore, the flat-bottom Lorentz-like potentials are recommended to represent cross-link restraints. It was also found that significant improvement of model quality upon the introduction of cross-link restraints is obtained when the sum of differences of indices of cross-linked residues exceeds 150.
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Affiliation(s)
- Mateusz Leśniewski
- Faculty
of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Maciej Pyrka
- Faculty
of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. 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, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Nguyen Truong Co
- Faculty
of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Yida Jiang
- College
of Chemistry and Molecular Engineering & Center for Quantitative
Biology & PKU-Tsinghua Center for Life Sciences & Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Zhou Gong
- Innovation
Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, 30 W. Xiao Hong Shan, Wuhan 430071, China
| | - Chun Tang
- College
of Chemistry and Molecular Engineering & Center for Quantitative
Biology & PKU-Tsinghua Center for Life Sciences & Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Adam Liwo
- 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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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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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: 15] [Impact Index Per Article: 15.0] [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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Xu X, Liu A, Liu S, Ma Y, Zhang X, Zhang M, Zhao J, Sun S, Sun X. Application of molecular dynamics simulation in self-assembled cancer nanomedicine. Biomater Res 2023; 27:39. [PMID: 37143168 PMCID: PMC10161522 DOI: 10.1186/s40824-023-00386-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
Self-assembled nanomedicine holds great potential in cancer theragnostic. The structures and dynamics of nanomedicine can be affected by a variety of non-covalent interactions, so it is essential to ensure the self-assembly process at atomic level. Molecular dynamics (MD) simulation is a key technology to link microcosm and macroscale. Along with the rapid development of computational power and simulation methods, scientists could simulate the specific process of intermolecular interactions. Thus, some experimental observations could be explained at microscopic level and the nanomedicine synthesis process would have traces to follow. This review not only outlines the concept, basic principle, and the parameter setting of MD simulation, but also highlights the recent progress in MD simulation for self-assembled cancer nanomedicine. In addition, the physicochemical parameters of self-assembly structure and interaction between various assembled molecules under MD simulation are also discussed. Therefore, this review will help advanced and novice researchers to quickly zoom in on fundamental information and gather some thought-provoking ideas to advance this subfield of self-assembled cancer nanomedicine.
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Affiliation(s)
- Xueli Xu
- School of Science, Shandong Jianzhu University, Jinan, 250101, China
| | - Ao Liu
- School of Science, Shandong Jianzhu University, Jinan, 250101, China
| | - Shuangqing Liu
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Yanling Ma
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Xinyu Zhang
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Meng Zhang
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Jinhua Zhao
- School of Science, Shandong Jianzhu University, Jinan, 250101, China
| | - Shuo Sun
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, 02115, USA
| | - Xiao Sun
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China.
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5
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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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/27/2022] [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
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6
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Biskupek I, Czaplewski C, Sawicka J, Iłowska E, Dzierżyńska M, Rodziewicz-Motowidło S, Liwo A. Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model. Biomolecules 2022; 12:1140. [PMID: 36009034 PMCID: PMC9406146 DOI: 10.3390/biom12081140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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Affiliation(s)
| | | | | | | | | | | | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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7
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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8
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Automated Protein Secondary Structure Assignment from C α Positions Using Neural Networks. Biomolecules 2022; 12:biom12060841. [PMID: 35740966 PMCID: PMC9220970 DOI: 10.3390/biom12060841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
The assignment of secondary structure elements in protein conformations is necessary to interpret a protein model that has been established by computational methods. The process essentially involves labeling the amino acid residues with H (Helix), E (Strand), or C (Coil, also known as Loop). When particular atoms are absent from an input protein structure, the procedure becomes more complicated, especially when only the alpha carbon locations are known. Various techniques have been tested and applied to this problem during the last forty years. The application of machine learning techniques is the most recent trend. This contribution presents the HECA classifier, which uses neural networks to assign protein secondary structure types. The technique exclusively employs Cα coordinates. The Keras (TensorFlow) library was used to implement and train the neural network model. The BioShell toolkit was used to calculate the neural network input features from raw coordinates. The study’s findings show that neural network-based methods may be successfully used to take on structure assignment challenges when only Cα trace is available. Thanks to the careful selection of input features, our approach’s accuracy (above 97%) exceeded that of the existing methods.
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