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Nithin C, Fornari RP, Pilla SP, Wroblewski K, Zalewski M, Madaj R, Kolinski A, Macnar JM, Kmiecik S. Exploring protein functions from structural flexibility using CABS-flex modeling. Protein Sci 2024; 33:e5090. [PMID: 39194135 DOI: 10.1002/pro.5090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/06/2024] [Accepted: 06/10/2024] [Indexed: 08/29/2024]
Abstract
Understanding protein function often necessitates characterizing the flexibility of protein structures. However, simulating protein flexibility poses significant challenges due to the complex dynamics of protein systems, requiring extensive computational resources and accurate modeling techniques. In response to these challenges, the CABS-flex method has been developed as an efficient modeling tool that combines coarse-grained simulations with all-atom detail. Available both as a web server and a standalone package, CABS-flex is dedicated to a wide range of users. The web server version offers an accessible interface for straightforward tasks, while the standalone command-line program is designed for advanced users, providing additional features, analytical tools, and support for handling large systems. This paper examines the application of CABS-flex across various structure-function studies, facilitating investigations into the interplay among protein structure, dynamics, and function in diverse research fields. We present an overview of the current status of the CABS-flex methodology, highlighting its recent advancements, practical applications, and forthcoming challenges.
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Affiliation(s)
- Chandran Nithin
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Rocco Peter Fornari
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Smita P Pilla
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Karol Wroblewski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Mateusz Zalewski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Rafał Madaj
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Kolinski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Joanna M Macnar
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
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2
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Majewski M, Pérez A, Thölke P, Doerr S, Charron NE, Giorgino T, Husic BE, Clementi C, Noé F, De Fabritiis G. Machine learning coarse-grained potentials of protein thermodynamics. Nat Commun 2023; 14:5739. [PMID: 37714883 PMCID: PMC10504246 DOI: 10.1038/s41467-023-41343-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/29/2023] [Indexed: 09/17/2023] Open
Abstract
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics.
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Affiliation(s)
- Maciej Majewski
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
- Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain
| | - Adrià Pérez
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
- Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain
| | - Philipp Thölke
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Stefan Doerr
- Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain
| | - Nicholas E Charron
- Department of Physics, Rice University, Houston, TX, 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA
- Department of Physics, FU Berlin, Arnimallee 12, 14195, Berlin, Germany
| | - Toni Giorgino
- Biophysics Institute, National Research Council (CNR-IBF), 20133, Milan, Italy
| | - Brooke E Husic
- Department of Mathematics and Computer Science, FU Berlin, Arnimallee 12, 14195, Berlin, Germany
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
- Princeton Center for Theoretical Science, Princeton University, Princeton, NJ, 08540, USA
- Center for the Physics of Biological Function, Princeton University, Princeton, NJ, 08540, USA
| | - Cecilia Clementi
- Department of Physics, Rice University, Houston, TX, 77005, USA.
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA.
- Department of Physics, FU Berlin, Arnimallee 12, 14195, Berlin, Germany.
- Department of Chemistry, Rice University, Houston, TX, 77005, USA.
| | - Frank Noé
- Department of Physics, FU Berlin, Arnimallee 12, 14195, Berlin, Germany.
- Department of Mathematics and Computer Science, FU Berlin, Arnimallee 12, 14195, Berlin, Germany.
- Department of Chemistry, Rice University, Houston, TX, 77005, USA.
- Microsoft Research AI4Science, Karl-Liebknecht Str. 32, 10178, Berlin, Germany.
| | - Gianni De Fabritiis
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain.
- Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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3
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Huang Z, Cui X, Xia Y, Zhao K, Zhang G. Pathfinder: Protein folding pathway prediction based on conformational sampling. PLoS Comput Biol 2023; 19:e1011438. [PMID: 37695768 PMCID: PMC10513300 DOI: 10.1371/journal.pcbi.1011438] [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: 05/04/2023] [Revised: 09/21/2023] [Accepted: 08/17/2023] [Indexed: 09/13/2023] Open
Abstract
The study of protein folding mechanism is a challenge in molecular biology, which is of great significance for revealing the movement rules of biological macromolecules, understanding the pathogenic mechanism of folding diseases, and designing protein engineering materials. Based on the hypothesis that the conformational sampling trajectory contain the information of folding pathway, we propose a protein folding pathway prediction algorithm named Pathfinder. Firstly, Pathfinder performs large-scale sampling of the conformational space and clusters the decoys obtained in the sampling. The heterogeneous conformations obtained by clustering are named seed states. Then, a resampling algorithm that is not constrained by the local energy basin is designed to obtain the transition probabilities of seed states. Finally, protein folding pathways are inferred from the maximum transition probabilities of seed states. The proposed Pathfinder is tested on our developed test set (34 proteins). For 11 widely studied proteins, we correctly predicted their folding pathways and specifically analyzed 5 of them. For 13 proteins, we predicted their folding pathways to be further verified by biological experiments. For 6 proteins, we analyzed the reasons for the low prediction accuracy. For the other 4 proteins without biological experiment results, potential folding pathways were predicted to provide new insights into protein folding mechanism. The results reveal that structural analogs may have different folding pathways to express different biological functions, homologous proteins may contain common folding pathways, and α-helices may be more prone to early protein folding than β-strands.
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Affiliation(s)
- Zhaohong Huang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Xinyue Cui
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Yuhao Xia
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Kailong Zhao
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Guijun Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
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4
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Kuczera K, Szoszkiewicz R, Shaffer CL, Jas GS. GB1 hairpin kinetics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction. J Biomol Struct Dyn 2023; 41:11671-11680. [PMID: 36591705 DOI: 10.1080/07391102.2022.2163427] [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: 10/19/2022] [Accepted: 12/22/2022] [Indexed: 01/03/2023]
Abstract
We have performed molecular dynamics (MD) and replica-exchange (REMD) simulations of folding of the GB1 hairpin peptide in aqueous solution. REMD results were consistent with a cooperative zipper folding model. 120 μ s MD trajectories at 320 K yielded relaxation times of 1.8 μ s and 100 ns, with the slower assigned to global folding. The MD folding/unfolding transitions also followed the cooperative zipper model, specifying nucleation at the central turn followed by consecutive hydrogen bond formation. Formation of hydrogen bonds and hydrophobic contacts were highly correlated. Coarse-grained kinetic models constructed with the Optimal Dimensionality Reduction (ODR) approach found a folding time of 3.3 μ s and unfolding time of 4.0 μ s . Additionally, relaxation times in the 130-170 ns range could be assigned to formation of the transition state and off-path intermediates. The unfolded state was the most highly populated and, significantly, most heterogenous, assembling the largest number of microstates, primarily composed of extended and turn structures. The folded state was also heterogenous, but a to a lesser degree, involving the fully folded and partially folded in-register hairpins at early stages of the zipper pathway. The transition state corresponded to the nucleated hairpin, with central turn and first beta-sheet hydrogen bond, while the off-path intermediates were off-register partial hairpins. Our simulation results were in excellent agreement with experimental data on folded fraction, relaxation time and folding mechanism. The new findings from this work suggest a highly cooperative zipper folding mechanism, nascent hairpin transition state and ∼100 ns relaxation related to intermediate formation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Krzysztof Kuczera
- Department of Chemistry, The University of Kansas, Lawrence, KS, USA
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Robert Szoszkiewicz
- Faculty of Chemistry, Biological and Chemical Research Centre University of Warsaw, Warsaw, Poland
| | - Christopher L Shaffer
- College of Pharmacy and Pediatric Clinical Pharmacology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Gouri S Jas
- College of Pharmacy and Pediatric Clinical Pharmacology, University of Nebraska Medical Center, Omaha, NE, USA
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5
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3β-Corner Stability by Comparative Molecular Dynamics Simulations. Int J Mol Sci 2022; 23:ijms231911674. [PMID: 36232976 PMCID: PMC9570037 DOI: 10.3390/ijms231911674] [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: 08/25/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
This study explored the mechanisms by which the stability of super-secondary structures of the 3β-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3β-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3β-corners from 330 structures was characterized by a root mean square deviation (RMSD) of less than 5 Å, a change in the gyration radius of no more than 5%, and the preservation of amino acid residues positioned within the allowed regions on the Ramachandran map. The studied structures retained their topologies throughout the MD experiments. Thus, the 3β-corner structure was found to be rather stable per se in a water environment, i.e., without the rest of a protein molecule, and can act as the nucleus or “ready-made” building block in protein folding. The 3β-corner can also be considered as an independent object for study in field of structural biology.
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Kondratyev M, Rudnev VR, Nikolsky KS, Stepanov AA, Petrovsky DV, Kulikova LI, Kopylov AT, Malsagova KA, Kaysheva AL. Atomic Simulation of the Binding of JAK1 and JAK2 with the Selective Inhibitor Ruxolitinib. Int J Mol Sci 2022; 23:ijms231810466. [PMID: 36142375 PMCID: PMC9504736 DOI: 10.3390/ijms231810466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022] Open
Abstract
Rheumatoid arthritis belongs to the group of chronic systemic autoimmune diseases characterized by the development of destructive synovitis and extra-articular manifestations. Cytokines regulate a wide range of inflammatory processes involved in the pathogenesis of rheumatoid arthritis and contribute to the induction of autoimmunity and chronic inflammation. Janus-associated kinase (JAK) and signal transducer and activator of transcription (STAT) proteins mediate cell signaling from cytokine receptors, and are involved in the pathogenesis of autoimmune and inflammatory diseases. Targeted small-molecule drugs that inhibit the functional activity of JAK proteins are used in clinical practice for the treatment of rheumatoid arthritis. In our study, we modeled the interactions of the small-molecule drug ruxolitinib with JAK1 and JAK2 isoforms and determined the binding selectivity using molecular docking. Molecular modeling data show that ruxolitinib selectively binds the JAK1 and JAK2 isoforms with a binding affinity of −8.3 and −8.0 kcal/mol, respectively. The stabilization of ligands in the cavity of kinases occurs primarily through hydrophobic interactions. The amino acid residues of the protein globules of kinases that are responsible for the correct positioning of the drug ruxolitinib and its retention have been determined.
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Affiliation(s)
- Maxim Kondratyev
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Vladimir R. Rudnev
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Kirill S. Nikolsky
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
| | - Alexander A. Stepanov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
| | - Denis V. Petrovsky
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
| | - Liudmila I. Kulikova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Arthur T. Kopylov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
| | - Kristina A. Malsagova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
- Correspondence: ; Tel.: +7-(499)-764-98-78
| | - Anna L. Kaysheva
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia
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7
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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: 25] [Impact Index Per Article: 8.3] [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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8
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Wang R, Liu M, Wang H, Xia J, Li H. GB Tags: Small Covalent Peptide Tags Based on Protein Fragment Reconstitution. Bioconjug Chem 2021; 32:1926-1934. [PMID: 34329559 DOI: 10.1021/acs.bioconjchem.1c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Developing peptide tags that can bind target proteins covalently under mild conditions is of great importance for a myriad of applications, ranging from chemical biology to biotechnology. Here we report the development of a small covalent peptide tag system, termed as GB tags, that can covalently label the target protein with high specificity and high yield under oxidizing conditions. The GB tags consist of a pair of short peptides, GN and GC (GN contains 45 residues and GC contains 19 residues). GN and GC, which are split from a parent protein GB1, can undergo protein fragment reconstitution to reconstitute the folded structure of the parent protein spontaneously. The engineered cysteines in GN and GC can readily form a disulfide bond oxidized by air oxygen after protein reconstitution. Using thermally stable variants of GB1, we identified two pairs of GB tags that display improved thermodynamic stability and binding affinity. They can serve as efficient covalent peptide tags for various applications, including specific labeling of mammalian cell surface receptors. We anticipate that these new GB tags will find applications in biochemical labeling as well as biomaterials, such as protein hydrogels.
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Affiliation(s)
- Ruidi Wang
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada.,State Key Laboratory of Supramolecular Structure and Materials College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Miao Liu
- Department of Chemistry, Chinese University of Hong Kong, Hong Kong SRC, P. R. China
| | - Han Wang
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Jiang Xia
- Department of Chemistry, Chinese University of Hong Kong, Hong Kong SRC, P. R. China
| | - Hongbin Li
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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9
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Santo AAE, Feliciano GT. Genetic Algorithms Applied to Thermodynamic Rational Design of Mimetic Antibodies Based on the GB1 Domain of Streptococcal Protein G: An Atomistic Simulation Study. J Phys Chem B 2021; 125:7985-7996. [PMID: 34264671 DOI: 10.1021/acs.jpcb.1c03324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of mimetic antibodies (MA) capable of combining the high affinity and selectivity of antibodies with the small size of the peptides has enormous potential for applications in current biotechnology. In this work, we demonstrate that in silico MA design is possible through genetic algorithms (GA) developed from shell scripts capable of combining software commonly used for atomistic simulation. Our results demonstrate that, using the GB1 domain of the streptococcal G protein as a model, it is possible to optimize the molecular recognition capacity of a large MA population in a few generations. In the first case, GA was able to generate 10 MA with binding free energy (BFE) less than the vascular endothelial cell growth factor conjugated with the fms-type tyrosine kinase receptor. In the second case, it generated 13 MA with BFE less than that of the hepatitis C-E2 viral envelope conjugate with the antibody. Through the GA developed in this work, we demonstrate the use of a new protocol, capable of guiding experimental methods for the design of bioactive peptides that can assist in the development of new therapeutic molecules.
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Affiliation(s)
- Anderson A E Santo
- Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil
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10
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Bedford JT, Poutsma J, Diawara N, Greene LH. The nature of persistent interactions in two model β-grasp proteins reveals the advantage of symmetry in stability. J Comput Chem 2021; 42:600-607. [PMID: 33534913 DOI: 10.1002/jcc.26477] [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: 07/13/2020] [Revised: 10/27/2020] [Accepted: 11/22/2020] [Indexed: 01/25/2023]
Abstract
Two proteins within the β-grasp superfamily, the B1-domain of protein G and the small archaeal modifier protein 1, were investigated to elucidate the key determinants of structural stability at the level of individual interactions. These symmetrical proteins both contain two β-hairpins which form a sheet flanked by a central α-helix. They were subjected to high temperature molecular dynamics simulations and the detailed behavior of each long-range interaction was characterized. The results revealed that in GB1 the most stable region was the C-terminal hairpin and in SAMP1 it was the opposite, the N-terminal hairpin. Experimental results for GB1 support this finding. In conclusion, it appears that the difference in the location and number of hydrophobic interactions dictate the differential stability which is accommodated due to structural symmetry of the β-grasp fold. Thus, the hairpins are interchangeable and in nature this lends itself to adaptability and flexibility.
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11
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Badaczewska-Dawid AE, Kolinski A, Kmiecik S. Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASS. Methods Mol Biol 2021; 2165:337-353. [PMID: 32621235 DOI: 10.1007/978-1-0716-0708-4_20] [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] [Indexed: 12/17/2022]
Abstract
Conformational flexibility of protein structures can play an important role in protein function. The flexibility is often studied using computational methods since experimental characterization can be difficult. Depending on protein system size, computational tools may require large computational resources or significant simplifications in the modeled systems to speed up calculations. In this work, we present the protocols for efficient simulations of flexibility of folded protein structures that use coarse-grained simulation tools of different resolutions: medium, represented by CABS-flex, and low, represented by SUPRASS. We test the protocols using a set of 140 globular proteins and compare the results with structure fluctuations observed in MD simulations, ENM modeling, and NMR ensembles. As demonstrated, CABS-flex predictions show high correlation to experimental and MD simulation data, while SURPASS is less accurate but promising in terms of future developments.
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Affiliation(s)
- Aleksandra E Badaczewska-Dawid
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland.,Department of Chemistry, Iowa State University, Ames, IA, USA
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland.
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12
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Becerra D, Butyaev A, Waldispühl J. Fast and flexible coarse-grained prediction of protein folding routes using ensemble modeling and evolutionary sequence variation. Bioinformatics 2020; 36:1420-1428. [PMID: 31584628 DOI: 10.1093/bioinformatics/btz743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/22/2019] [Accepted: 09/28/2019] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION Protein folding is a dynamic process through which polypeptide chains reach their native 3D structures. Although the importance of this mechanism is widely acknowledged, very few high-throughput computational methods have been developed to study it. RESULTS In this paper, we report a computational platform named P3Fold that combines statistical and evolutionary information for predicting and analyzing protein folding routes. P3Fold uses coarse-grained modeling and efficient combinatorial schemes to predict residue contacts and evaluate the folding routes of a protein sequence within minutes or hours. To facilitate access to this technology, we devise graphical representations and implement an interactive web interface that allows end-users to leverage P3Fold predictions. Finally, we use P3Fold to conduct large and short scale experiments on the human proteome that reveal the broad conservation and variations of structural intermediates within protein families. AVAILABILITY AND IMPLEMENTATION A Web server of P3Fold is freely available at http://csb.cs.mcgill.ca/P3Fold. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David Becerra
- School of Computer Science, McGill University, Montréal, QC H3A 0E9, Canada
| | - Alexander Butyaev
- School of Computer Science, McGill University, Montréal, QC H3A 0E9, Canada
| | - Jérôme Waldispühl
- School of Computer Science, McGill University, Montréal, QC H3A 0E9, Canada
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13
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Docking interactions determine early cleavage events in insulin proteolysis by pepsin: Experiment and simulation. Int J Biol Macromol 2020; 149:1151-1160. [PMID: 32001282 DOI: 10.1016/j.ijbiomac.2020.01.253] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/20/2020] [Accepted: 01/25/2020] [Indexed: 12/12/2022]
Abstract
In silico modelling of cascade enzymatic proteolysis is an exceedingly complex and challenging task. Here, we study partial proteolysis of insulin by pepsin: a process leading to the release of a highly amyloidogenic two chain 'H-fragment'. The H-fragment retains several cleavage sites for pepsin. However, under favorable conditions H-monomers rapidly self-assemble into proteolysis-resistant amyloid fibrils whose composition provides snapshots of early and intermediate stages of the proteolysis. In this work, we report a remarkable agreement of experimentally determined and simulation-predicted cleavage sites on different stages of the proteolysis. Prediction of cleavage sites was based on the comprehensive analysis of the docking interactions from direct simulation of coupled folding and binding of insulin (or its cleaved derivatives) to pepsin. The most frequent interactions were found to be between the pepsin's active site, or its direct vicinity, and the experimentally determined insulin cleavage sites, which suggest that the docking interactions govern the proteolytic process.
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Kurcinski M, Badaczewska‐Dawid A, Kolinski M, Kolinski A, Kmiecik S. Flexible docking of peptides to proteins using CABS-dock. Protein Sci 2020; 29:211-222. [PMID: 31682301 PMCID: PMC6933849 DOI: 10.1002/pro.3771] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022]
Abstract
Molecular docking of peptides to proteins can be a useful tool in the exploration of the possible peptide binding sites and poses. CABS-dock is a method for protein-peptide docking that features significant conformational flexibility of both the peptide and the protein molecules during the peptide search for a binding site. The CABS-dock has been made available as a web server and a standalone package. The web server is an easy to use tool with a simple web interface. The standalone package is a command-line program dedicated to professional users. It offers a number of advanced features, analysis tools and support for large-sized systems. In this article, we outline the current status of the CABS-dock method, its recent developments, applications, and challenges ahead.
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Affiliation(s)
- Mateusz Kurcinski
- Faculty of Chemistry, Biological and Chemical Research CenterUniversity of WarsawWarsawPoland
| | | | - Michal Kolinski
- Bioinformatics Laboratory, Mossakowski Medical Research CentrePolish Academy of SciencesWarsawPoland
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research CenterUniversity of WarsawWarsawPoland
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research CenterUniversity of WarsawWarsawPoland
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15
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Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications. Int J Mol Sci 2019; 20:ijms20153774. [PMID: 31375023 PMCID: PMC6696403 DOI: 10.3390/ijms20153774] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.
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16
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Geng H, Chen F, Ye J, Jiang F. Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins. Comput Struct Biotechnol J 2019; 17:1162-1170. [PMID: 31462972 PMCID: PMC6709365 DOI: 10.1016/j.csbj.2019.07.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/07/2019] [Accepted: 07/23/2019] [Indexed: 12/21/2022] Open
Abstract
Compared with rapid accumulation of protein sequences from high-throughput DNA sequencing, obtaining experimental 3D structures of proteins is still much more difficult, making protein structure prediction (PSP) potentially very useful. Currently, a vast majority of PSP efforts are based on data mining of known sequences, structures and their relationships (informatics-based). However, if closely related template is not available, these methods are usually much less reliable than experiments. They may also be problematic in predicting the structures of naturally occurring or designed peptides. On the other hand, physics-based methods including molecular dynamics (MD) can utilize our understanding of detailed atomic interactions determining biomolecular structures. In this mini-review, we show that all-atom MD can predict structures of cyclic peptides and other peptide foldamers with accuracy similar to experiments. Then, some notable successes in reproducing experimental 3D structures of small proteins through MD simulations (some with replica-exchange) of the folding were summarized. We also describe advancements of MD-based refinement of structure models, and the integration of limited experimental or bioinformatics data into MD-based structure modeling.
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Affiliation(s)
- Hao Geng
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Fangfang Chen
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China
| | - Jing Ye
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China
| | - Fan Jiang
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- NanoAI Biotech Co.,Ltd., Silicon Valley Compound, Longhua District, Shenzhen 518109, China
- Corresponding author at: Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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17
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Cheng Q, Joung I, Lee J, Kuwajima K, Lee J. Exploring the Folding Mechanism of Small Proteins GB1 and LB1. J Chem Theory Comput 2019; 15:3432-3449. [DOI: 10.1021/acs.jctc.8b01163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qianyi Cheng
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - InSuk Joung
- Department of Chemistry, Kangwon National University, Chuncheon 24341, South Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Juyong Lee
- Department of Chemistry, Kangwon National University, Chuncheon 24341, South Korea
| | - Kunihiro Kuwajima
- Department of Physics, University of Tokyo, Tokyo 113-0033, Japan
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Jooyoung Lee
- Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul 02455, South Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, South Korea
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18
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Holtan JP, Teigen K, Aukrust I, Bragadóttir R, Houge G. Dominant ARL3-related retinitis pigmentosa. Ophthalmic Genet 2019; 40:124-128. [PMID: 30932721 DOI: 10.1080/13816810.2019.1586965] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
PURPOSE To clinically and genetically characterise a second family with dominant ARL3-related retinitis pigmentosa due to a specific ARL3 missense variant, p.(Tyr90Cys). METHODS Clinical examination included optical coherence tomography, electroretinography, and ultra-wide field retinal imaging with autofluorescence. Retrospective data were collected from the registry of inherited retinal diseases at Oslo university hospital. DNA was analysed by whole-exome sequencing and Sanger sequencing. The ARL3 missense variant was visualized in a 3D-protein structure. RESULTS The phenotype was non-syndromic retinitis pigmentosa with cataract associated with early onset of decreased central vision and central retinal thinning. Sanger sequencing confirmed the presence of a de novo ARL3 missense variant p.(Tyr90Cys) in the index patient and his affected son. We did not find any other cases with rare ARL3 variants in a cohort of 431 patients with retinitis pigmentosa-like disease. By visualizing Tyr90 in the 3D protein structure, it seems to play an important role in packing of the α/β structure of ADP-ribosylation factor-like 3 (ARL3). When changing Tyr90 to cysteine, we observe a loss of interactions in the core of the α/β structure that is likely to affect folding and stability of ARL3. CONCLUSION Our study confirms that the ARL3 missense variant p.(Tyr90Cys) causes retinitis pigmentosa. In 2016, Strom et al. reported the exact same variant in a mother and two children with RP, labelled ?RP83 in the OMIM database. Now the questionmark can be removed, and ARL3 should be added to the list of genes that may cause non-syndromic dominant retinitis pigmentosa.
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Affiliation(s)
- Josephine Prener Holtan
- a Department of Ophthalmology , Oslo University Hospital , Oslo , Norway.,b Institute of Clinical Medicine , University of Oslo , Oslo , Norway
| | - Knut Teigen
- c Department of Biomedicine , University of Bergen , Bergen , Norway
| | - Ingvild Aukrust
- d Department of Medical Genetics , Haukeland University Hospital , Bergen , Norway
| | - Ragnheiður Bragadóttir
- a Department of Ophthalmology , Oslo University Hospital , Oslo , Norway.,b Institute of Clinical Medicine , University of Oslo , Oslo , Norway
| | - Gunnar Houge
- d Department of Medical Genetics , Haukeland University Hospital , Bergen , Norway
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19
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Ebrahim-Habibi MB, Ghobeh M, Mahyari FA, Rafii-Tabar H, Sasanpour P. An investigation into non-covalent functionalization of a single-walled carbon nanotube and a graphene sheet with protein G:A combined experimental and molecular dynamics study. Sci Rep 2019; 9:1273. [PMID: 30718580 PMCID: PMC6362288 DOI: 10.1038/s41598-018-37311-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/06/2018] [Indexed: 12/15/2022] Open
Abstract
Investigation of non-covalent interaction of hydrophobic surfaces with the protein G (PrG) is necessary due to their frequent utilization in immunosensors and ELISA. It has been confirmed that surfaces, including carbonous-nanostructures (CNS) could orient proteins for a better activation. Herein, PrG interaction with single-walled carbon nanotube (SWCNT) and graphene (Gra) nanostructures was studied by employing experimental and MD simulation techniques. It is confirmed that the PrG could adequately interact with both SWCNT and Gra and therefore fine dispersion for them was achieved in the media. Results indicated that even though SWCNT was loaded with more content of PrG in comparison with the Gra, the adsorption of the PrG on Gra did not induce significant changes in the IgG tendency. Several orientations of the PrG were adopted in the presence of SWCNT or Gra; however, SWCNT could block the PrG-FcR. Moreover, it was confirmed that SWCNT reduced the α-helical structure content in the PrG. Reduction of α-helical structure of the PrG and improper orientation of the PrG-SWCNT could remarkably decrease the PrG tendency to the Fc of the IgG. Importantly, the Gra could appropriately orient the PrG by both exposing the PrG-FcR and also by blocking the fragment of the PrG that had tendency to interact with Fab in IgG.
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Affiliation(s)
- Mohammad-Bagher Ebrahim-Habibi
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Ghobeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Hashem Rafii-Tabar
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Pezhman Sasanpour
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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20
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Ciemny MP, Badaczewska-Dawid AE, Pikuzinska M, Kolinski A, Kmiecik S. Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields. Int J Mol Sci 2019; 20:E606. [PMID: 30708941 PMCID: PMC6386871 DOI: 10.3390/ijms20030606] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/20/2022] Open
Abstract
The description of protein disordered states is important for understanding protein folding mechanisms and their functions. In this short review, we briefly describe a simulation approach to modeling protein interactions, which involve disordered peptide partners or intrinsically disordered protein regions, and unfolded states of globular proteins. It is based on the CABS coarse-grained protein model that uses a Monte Carlo (MC) sampling scheme and a knowledge-based statistical force field. We review several case studies showing that description of protein disordered states resulting from CABS simulations is consistent with experimental data. The case studies comprise investigations of protein⁻peptide binding and protein folding processes. The CABS model has been recently made available as the simulation engine of multiscale modeling tools enabling studies of protein⁻peptide docking and protein flexibility. Those tools offer customization of the modeling process, driving the conformational search using distance restraints, reconstruction of selected models to all-atom resolution, and simulation of large protein systems in a reasonable computational time. Therefore, CABS can be combined in integrative modeling pipelines incorporating experimental data and other modeling tools of various resolution.
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Affiliation(s)
- Maciej Pawel Ciemny
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | | | - Monika Pikuzinska
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
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21
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Abstract
The folding simulations of three ββα-motifs and β-barrel structured proteins (NTL9, NuG2b, and CspA) were performed to determine the important roles of native and nonnative contacts in protein folding.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Weiliang Zhu
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
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22
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Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci 2018; 19:ijms19113496. [PMID: 30404229 PMCID: PMC6274762 DOI: 10.3390/ijms19113496] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022] Open
Abstract
Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this minireview, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions, and highly simplified structure-based elastic network models of protein flexibility. In contrast to classical all-atom molecular dynamics, the modeling strategies discussed here allow the quite accurate modeling of much larger systems and longer-time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.
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23
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Martins de Oliveira V, Godoi Contessoto VD, Bruno da Silva F, Zago Caetano DL, Jurado de Carvalho S, Pereira Leite VB. Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models. Biophys J 2018; 114:65-75. [PMID: 29320697 PMCID: PMC5984902 DOI: 10.1016/j.bpj.2017.11.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/20/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
The importance of charge-charge interactions in the thermal stability of proteins is widely known. pH and ionic strength play a crucial role in these electrostatic interactions, as well as in the arrangement of ionizable residues in each protein-folding stage. In this study, two coarse-grained models were used to evaluate the effect of pH and salt concentration on the thermal stability of a protein G variant (1PGB-QDD), which was chosen due to the quantity of experimental data exploring these effects on its stability. One of these coarse-grained models, the TKSA, calculates the electrostatic free energy of the protein in the native state via the Tanford-Kirkwood approach for each residue. The other one, CpHMD-SBM, uses a Coulomb screening potential in addition to the structure-based model Cα. Both models simulate the system in constant pH. The comparison between the experimental stability analysis and the computational results obtained by these simple models showed a good agreement. Through the TKSA method, the role of each charged residue in the protein's thermal stability was inferred. Using CpHMD-SBM, it was possible to evaluate salt and pH effects throughout the folding process. Finally, the computational pKa values were calculated by both methods and presented a good level of agreement with the experiments. This study provides, to our knowledge, new information and a comprehensive description of the electrostatic contribution to protein G stability.
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Affiliation(s)
- Vinícius Martins de Oliveira
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Vinícius de Godoi Contessoto
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil; Brazilian Bioethanol Science and Technology Laboratory- (CTBE), Campinas, Brazil
| | - Fernando Bruno da Silva
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Daniel Lucas Zago Caetano
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Sidney Jurado de Carvalho
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Vitor Barbanti Pereira Leite
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil.
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24
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Kurcinski M, Blaszczyk M, Ciemny MP, Kolinski A, Kmiecik S. A protocol for CABS-dock protein-peptide docking driven by side-chain contact information. Biomed Eng Online 2017; 16:73. [PMID: 28830545 PMCID: PMC5568604 DOI: 10.1186/s12938-017-0363-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Background The characterization of protein–peptide interactions is a challenge for computational molecular docking. Protein–peptide docking tools face at least two major difficulties: (1) efficient sampling of large-scale conformational changes induced by binding and (2) selection of the best models from a large set of predicted structures. In this paper, we merge an efficient sampling technique with external information about side-chain contacts to sample and select the best possible models. Methods In this paper we test a new protocol that uses information about side-chain contacts in CABS-dock protein–peptide docking. As shown in our recent studies, CABS-dock enables efficient modeling of large-scale conformational changes without knowledge about the binding site. However, the resulting set of binding sites and poses is in many cases highly diverse and difficult to score. Results As we demonstrate here, information about a single side-chain contact can significantly improve the prediction accuracy. Importantly, the imposed constraints for side-chain contacts are quite soft. Therefore, the developed protocol does not require precise contact information and ensures large-scale peptide flexibility in the broad contact area. Conclusions The demonstrated protocol provides the extension of the CABS-dock method that can be practically used in the structure prediction of protein–peptide complexes guided by the knowledge of the binding interface.
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Affiliation(s)
- Mateusz Kurcinski
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Maciej Blaszczyk
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Maciej Pawel Ciemny
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
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25
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Ciemny MP, Kurcinski M, Blaszczyk M, Kolinski A, Kmiecik S. Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif. Biomed Eng Online 2017; 16:71. [PMID: 28830442 PMCID: PMC5568603 DOI: 10.1186/s12938-017-0362-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Many protein–protein interactions are mediated by a short linear motif. Usually, amino acid sequences of those motifs are known or can be predicted. It is much harder to experimentally characterize or predict their structure in the bound form. In this work, we test a possibility of using flexible docking of a short linear motif to predict the interaction interface of the EphB4-EphrinB2 complex (a system extensively studied for its significance in tumor progression). Methods In the modeling, we only use knowledge about the motif sequence and experimental structures of EphB4-EphrinB2 complex partners. The proposed protocol enables efficient modeling of significant conformational changes in the short linear motif fragment during molecular docking simulation. For the docking simulations, we use the CABS-dock method for docking fully flexible peptides to flexible protein receptors (available as a server at http://biocomp.chem.uw.edu.pl/CABSdock/). Based on the docking result, the protein–protein complex is reconstructed and refined. Results Using this novel protocol, we obtained an accurate EphB4-EphrinB2 interaction model. Conclusions The results show that the CABS-dock method may be useful as the primary docking tool in specific protein–protein docking cases similar to EphB4-EphrinB2 complex—that is, where a short linear motif fragment can be identified.
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Affiliation(s)
- Maciej Pawel Ciemny
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, Poland
| | - Mateusz Kurcinski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Maciej Blaszczyk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
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26
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Berkovich R, Mondal J, Paster I, Berne BJ. Simulated Force Quench Dynamics Shows GB1 Protein Is Not a Two State Folder. J Phys Chem B 2017; 121:5162-5173. [PMID: 28453938 DOI: 10.1021/acs.jpcb.7b00610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single molecule force spectroscopy is a useful technique for investigating mechanically induced protein unfolding and refolding under reduced forces by monitoring the end-to-end distance of the protein. The data is often interpreted via a "two-state" model based on the assumption that the end-to-end distance alone is a good reaction coordinate and the thermodynamic behavior is then ascribed to the free energy as a function of this one reaction coordinate. In this paper, we determined the free energy surface (PMF) of GB1 protein from atomistic simulations in explicit solvent under different applied forces as a function of two collective variables (the end-to-end-distance, and the fraction of native contacts ρ). The calculated 2-d free energy surfaces exhibited several distinct states, or basins, mostly visible along the ρ coordinate. Brownian dynamics (BD) simulations on the smoothed free energy surface show that the protein visits a metastable molten globule state and is thus a three state folder, not the two state folder inferred using the end-to-end distance as the sole reaction coordinate. This study lends support to recent experiments that suggest that GB1 is not a two-state folder.
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Affiliation(s)
- Ronen Berkovich
- Department of Chemical Engineering, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences , Hyderabad, India
| | - Inga Paster
- Department of Chemical Engineering, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - B J Berne
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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27
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Kouza M, Lan PD, Gabovich AM, Kolinski A, Li MS. Switch from thermal to force-driven pathways of protein refolding. J Chem Phys 2017; 146:135101. [DOI: 10.1063/1.4979201] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Walters CR, Szantai-Kis DM, Zhang Y, Reinert ZE, Horne WS, Chenoweth DM, Petersson EJ. The effects of thioamide backbone substitution on protein stability: a study in α-helical, β-sheet, and polyproline II helical contexts. Chem Sci 2017; 8:2868-2877. [PMID: 28553525 PMCID: PMC5428018 DOI: 10.1039/c6sc05580j] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/24/2017] [Indexed: 12/17/2022] Open
Abstract
Thioamides are single atom substitutions of the peptide bond that serve as versatile probes of protein structure. Effective use of thioamides requires a robust understanding of the impact that the substitution has on a protein of interest. However, the thermodynamic effects of thioamide incorporation have only been studied in small structural motifs, and their influence on secondary structure in the context of full-length proteins is not known. Here we describe a comprehensive survey of thioamide substitutions in three benchmark protein systems (calmodulin, the B1 domain of protein G, and collagen) featuring the most prevalent secondary structure motifs: α-helix, β-sheet, and polyproline type II helix. We find that in most cases, effects on thermostability can be understood in terms of the positioning and local environment of the thioamide relative to proximal structural elements and hydrogen bonding networks. These observations set the stage for the rational design of thioamide substituted proteins with predictable stabilities.
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Affiliation(s)
- Christopher R Walters
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
| | - D Miklos Szantai-Kis
- Biochemistry and Molecular Biophysics Graduate Group , University of Pennsylvania , 3700 Hamilton Walk , Philadelphia , PA 19104 , USA
| | - Yitao Zhang
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
| | - Zachary E Reinert
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , PA 15260 , USA
| | - W Seth Horne
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , PA 15260 , USA
| | - David M Chenoweth
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
| | - E James Petersson
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
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29
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Makowski M, Liwo A, Scheraga HA. Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains. J Phys Chem B 2017; 121:379-390. [PMID: 28000446 DOI: 10.1021/acs.jpcb.6b08541] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physics-based potentials of side-chain-side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge-dipole or dipole-dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains. The model used in this work reproduces all features of the interacting pairs. The UNited RESidue force field with the new side-chain-side-chain interaction potentials was preliminarily tested with the N-terminal part of the B-domain of staphylococcal protein A (PDBL 1BDD ; a three-α-helix bundle) and UPF0291 protein YnzC from Bacillus subtilis (PDB: 2HEP ; an α-helical hairpin).
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Affiliation(s)
- Mariusz Makowski
- 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
| | - Harold A Scheraga
- Baker laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States
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30
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Kmiecik S, Kolinski A. One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model. Methods Mol Biol 2017; 1484:83-113. [PMID: 27787822 DOI: 10.1007/978-1-4939-6406-2_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps the most successful strategy to overcome the inefficiency problem is multiscale modeling to merge all-atom and coarse-grained models. This chapter describes a well-established CABS coarse-grained protein model. The CABS (C-Alpha, C-Beta, and Side chains) model assumes a 2-4 united-atom representation of amino acids, knowledge-based force field (derived from the statistical regularities seen in known protein sequences and structures) and efficient Monte Carlo sampling schemes (MC dynamics, MC replica-exchange, and combinations). A particular emphasis is given to the unique design of the CABS force-field, which is largely defined using one-dimensional structural properties of proteins, including protein secondary structure. This chapter also presents CABS-based modeling methods, including multiscale tools for de novo structure prediction, modeling of protein dynamics and prediction of protein-peptide complexes. CABS-based tools are freely available at http://biocomp.chem.uw.edu.pl/tools.
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Affiliation(s)
- Sebastian Kmiecik
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warszawa, 02-093, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warszawa, 02-093, Poland.
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31
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Pulawski W, Jamroz M, Kolinski M, Kolinski A, Kmiecik S. Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model. J Chem Inf Model 2016; 56:2207-2215. [PMID: 27775349 DOI: 10.1021/acs.jcim.6b00350] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics, and interactions). Here we introduce an extension of the CABS representation and force field (CABS-membrane) to the modeling of the effect of the biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane. In the resulting trajectories, we have found models close to the experimental membrane structures. We also attempted to select the correctly folded models using simple filtering followed by structural clustering combined with reconstruction to the all-atom representation and all-atom scoring. The CABS-membrane model is a promising approach for further development toward modeling of large protein-membrane systems.
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Affiliation(s)
- Wojciech Pulawski
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Jamroz
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences , Pawinskiego 5, 02-106 Warsaw, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
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32
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Mozolewska MA, Krupa P, Zaborowski B, Liwo A, Lee J, Joo K, Czaplewski C. Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field. J Chem Inf Model 2016; 56:2263-2279. [DOI: 10.1021/acs.jcim.6b00189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Paweł Krupa
- 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
- Center
for In Silico Protein Structure and School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Jooyoung Lee
- Center
for In Silico Protein Structure and 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, 80-308 Gdańsk, Poland
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33
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Sacquin-Mora S. Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus? J R Soc Interface 2016; 12:rsif.2015.0876. [PMID: 26577596 DOI: 10.1098/rsif.2015.0876] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The determination of a protein's folding nucleus, i.e. a set of native contacts playing an important role during its folding process, remains an elusive yet essential problem in biochemistry. In this work, we investigate the mechanical properties of 70 protein structures belonging to 14 protein families presenting various folds using coarse-grain Brownian dynamics simulations. The resulting rigidity profiles combined with multiple sequence alignments show that a limited set of rigid residues, which we call the consensus nucleus, occupy conserved positions along the protein sequence. These residues' side chains form a tight interaction network within the protein's core, thus making our consensus nuclei potential folding nuclei. A review of experimental and theoretical literature shows that most (above 80%) of these residues were indeed identified as folding nucleus member in earlier studies.
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Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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34
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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35
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Sikosek T, Krobath H, Chan HS. Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches. PLoS Comput Biol 2016; 12:e1004960. [PMID: 27253392 PMCID: PMC4890782 DOI: 10.1371/journal.pcbi.1004960] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/04/2016] [Indexed: 11/18/2022] Open
Abstract
Deciphering the effects of nonsynonymous mutations on protein structure is central to many areas of biomedical research and is of fundamental importance to the study of molecular evolution. Much of the investigation of protein evolution has focused on mutations that leave a protein’s folded structure essentially unchanged. However, to evolve novel folds of proteins, mutations that lead to large conformational modifications have to be involved. Unraveling the basic biophysics of such mutations is a challenge to theory, especially when only one or two amino acid substitutions cause a large-scale conformational switch. Among the few such mutational switches identified experimentally, the one between the GA all-α and GB α+β folds is extensively characterized; but all-atom simulations using fully transferrable potentials have not been able to account for this striking switching behavior. Here we introduce an explicit-chain model that combines structure-based native biases for multiple alternative structures with a general physical atomic force field, and apply this construct to twelve mutants spanning the sequence variation between GA and GB. In agreement with experiment, we observe conformational switching from GA to GB upon a single L45Y substitution in the GA98 mutant. In line with the latent evolutionary potential concept, our model shows a gradual sequence-dependent change in fold preference in the mutants before this switch. Our analysis also indicates that a sharp GA/GB switch may arise from the orientation dependence of aromatic π-interactions. These findings provide physical insights toward rationalizing, predicting and designing evolutionary conformational switches. The biological functions of globular proteins are intimately related to their folded structures and their associated conformational fluctuations. Evolution of new structures is an important avenue to new functions. Although many mutations do not change the folded state, experiments indicate that a single amino acid substitution can lead to a drastic change in the folded structure. The physics of this switch-like behavior remains to be elucidated. Here we develop a computational model for the relevant physical forces, showing that mutations can lead to new folds by passing through intermediate sequences where the old and new folds occur with varying probabilities. Our approach helps provide a general physical account of conformational switching in evolution and mutational effects on conformational dynamics.
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Affiliation(s)
- Tobias Sikosek
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Heinrich Krobath
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hue Sun Chan
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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36
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Zhang Y, Weber JK, Zhou R. Folding and Stabilization of Native-Sequence-Reversed Proteins. Sci Rep 2016; 6:25138. [PMID: 27113844 PMCID: PMC4844985 DOI: 10.1038/srep25138] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/06/2016] [Indexed: 11/29/2022] Open
Abstract
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we investigate how the reverse-sequences of native proteins might fold by examining a series of small proteins of increasing structural complexity (α-helix, β-hairpin, α-helix bundle, and α/β-protein). Employing a tandem protein structure prediction algorithmic and molecular dynamics simulation approach, we find that the ability of reverse sequences to adopt native-like folds is strongly influenced by protein size and the flexibility of the native hydrophobic core. For β-hairpins with reverse-sequences that fail to fold, we employ a simple mutational strategy for guiding stable hairpin formation that involves the insertion of amino acids into the β-turn region. This systematic look at reverse sequence duality sheds new light on the problem of protein sequence-structure mapping and may serve to inspire new protein design and protein structure prediction protocols.
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Affiliation(s)
- Yuanzhao Zhang
- Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China.,Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Jeffrey K Weber
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Ruhong Zhou
- Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China.,Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA.,Department of Chemistry, Columbia University, New York, NY 10027, USA
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37
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Yefremova Y, Al-Majdoub M, Opuni KF, Koy C, Yan Y, Gross M, Glocker MO. A Dynamic Model of pH-Induced Protein G'e Higher Order Structure Changes derived from Mass Spectrometric Analyses. Anal Chem 2016; 88:890-7. [PMID: 26606592 PMCID: PMC5201196 DOI: 10.1021/acs.analchem.5b03536] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To obtain insight into pH change-driven molecular dynamics, we studied the higher order structure changes of protein G'e at the molecular and amino acid residue levels in solution by using nanoESI- and IM-mass spectrometry, CD spectroscopy, and protein chemical modification reactions (protein footprinting). We found a dramatic change of the overall tertiary structure of protein G'e when the pH was changed from neutral to acidic, whereas its secondary structure features remained nearly invariable. Limited proteolysis and surface-topology mapping of protein G'e by fast photochemical oxidation of proteins (FPOP) under neutral and acidic conditions reveal areas where higher order conformational changes occur on the amino-acid residue level. Under neutral solution conditions, lower oxidation occurs for residues of the first linker region, whereas greater oxidative modifications occur for amino-acid residues of the IgG-binding domains I and II. We propose a dynamic model of pH-induced structural changes in which protein G'e at neutral pH adopts an overall tight conformation with all four domains packed in a firm assembly, whereas at acidic pH, the three IgG-binding domains form an elongated alignment, and the N-terminal, His-tag-carrying domain unfolds. At the same time the individual IgG-binding domains themselves seem to adopt a more compacted fold. As the secondary structure features are nearly unchanged at either pH, interchange between both conformations is highly reversible, explaining the high reconditioning power of protein G'e-based affinity chromatography columns.
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Affiliation(s)
- Yelena Yefremova
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | | | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Yuetian Yan
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 USA
| | - Michael Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 USA
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38
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Kurcinski M, Kolinski A, Kmiecik S. Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations. J Chem Theory Comput 2015; 10:2224-31. [PMID: 26580746 DOI: 10.1021/ct500287c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A complex of the phosphorylated kinase-inducible domain (pKID) with its interacting domain (KIX) is a model system for studies of mechanisms by which intrinsically unfolded proteins perform their functions. These mechanisms are not fully understood. Using an efficient coarse-grained model, ab initio simulations were performed of the coupled folding and binding of the pKID to the KIX. The simulations start from an unbound, randomly positioned and disordered pKID structure. During the simulations the pKID chain and its position remain completely unrestricted, while the KIX backbone is limited to near-native fluctuations. Ab initio simulations of such large-scale conformational transitions, unaffected by any knowledge about the bound pKID structure, remain inaccessible to classical simulations. Our simulations recover an ensemble of transient encounter complexes in good agreement with experimental results. We find that a key folding and binding step is linked to the formation of weak native interactions between a preformed nativelike fragment of a pKID helix and KIX surface. Once that nucleus forms, the pKID chain may condense from a largely disordered encounter ensemble to a natively bound and ordered conformation. The observed mechanism is reminiscent of a nucleation-condensation model, a common scenario for folding of globular proteins.
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Affiliation(s)
- Mateusz Kurcinski
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
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39
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ZHANG HUCHENG, LIANG WEIFENG, FAN HAITAO, YANG JUN, YANG GUOWEI, WANG XIAOJIE, CHEN LIANG, LIANG TAO. Immunological characterization and verification of recombinant streptococcal protein G. Mol Med Rep 2015; 12:6311-5. [DOI: 10.3892/mmr.2015.4162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 06/17/2015] [Indexed: 11/05/2022] Open
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40
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Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking. Methods 2015; 93:72-83. [PMID: 26165956 DOI: 10.1016/j.ymeth.2015.07.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/06/2015] [Accepted: 07/08/2015] [Indexed: 11/22/2022] Open
Abstract
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of protein-peptide interactions is usually divided into two stages: prediction of the binding site at a protein receptor surface, and then docking (and modeling) the peptide structure into the known binding site. This paper presents a comprehensive CABS-dock method for the simultaneous search of binding sites and flexible protein-peptide docking, available as a user's friendly web server. We present example CABS-dock results obtained in the default CABS-dock mode and using its advanced options that enable the user to increase the range of flexibility for chosen receptor fragments or to exclude user-selected binding modes from docking search. Furthermore, we demonstrate a strategy to improve CABS-dock performance by assessing the quality of models with classical molecular dynamics. Finally, we discuss the promising extensions and applications of the CABS-dock method and provide a tutorial appendix for the convenient analysis and visualization of CABS-dock results. The CABS-dock web server is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/.
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41
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Production of recombinant protein G through high-density fermentation of engineered bacteria as well as purification. Mol Med Rep 2015; 12:3132-8. [DOI: 10.3892/mmr.2015.3688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 02/11/2015] [Indexed: 11/05/2022] Open
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42
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Kmiecik S, Jamroz M, Kolinski M. Structure prediction of the second extracellular loop in G-protein-coupled receptors. Biophys J 2015; 106:2408-16. [PMID: 24896119 PMCID: PMC4052351 DOI: 10.1016/j.bpj.2014.04.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/26/2014] [Accepted: 04/17/2014] [Indexed: 12/29/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs.
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Affiliation(s)
- Sebastian Kmiecik
- University of Warsaw, Faculty of Chemistry, Laboratory of Theory of Biopolymers, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Jamroz
- University of Warsaw, Faculty of Chemistry, Laboratory of Theory of Biopolymers, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Mossakowski Medical Research Center, Polish Academy of Sciences, Bioinformatics Laboratory, Pawinskiego 5, 02-106 Warsaw, Poland.
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43
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Smerkova K, Vlcnovska M, Dostalova S, Milosavljevic V, Kopel P, Vaculovic T, Krizkova S, Vaculovicova M, Adam V, Kizek R. ELISA-like Analysis of Cisplatinated DNA Using Magnetic Separation. Nanobiomedicine (Rij) 2015; 2:10. [PMID: 29942374 PMCID: PMC5997378 DOI: 10.5772/61699] [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: 12/16/2014] [Accepted: 09/21/2015] [Indexed: 11/12/2022] Open
Abstract
Cisplatin belongs to the most widely used cytostatic drugs. The determination of the presence of the DNA-cisplatin adducts may not only signal the guanine-rich regions but also monitor the interaction reaction between DNA and the drug in terms of speed of interaction. In this work, the combined advantages of magnetic particles-based isolation/purification with fluorescent properties of quantum dots (QDs) and antibodies targeted on specific recognition of DNA-cisplatin adducts are demonstrated. The formation of a complex between magnetic particles with surface modified by anti-dsDNA antibody, cisplatin-modified DNA and QDs labelled anti-cisplatin-modified DNA antibody was suggested and optimized.
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Affiliation(s)
- Kristyna Smerkova
- Department of Chemistry and Biochemistry, Laboratory of Metallomics and Nanotechnology, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Marcela Vlcnovska
- Department of Chemistry and Biochemistry, Laboratory of Metallomics and Nanotechnology, Mendel University in Brno, Brno, Czech Republic
| | - Simona Dostalova
- Department of Chemistry and Biochemistry, Laboratory of Metallomics and Nanotechnology, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Vedran Milosavljevic
- Department of Chemistry and Biochemistry, Laboratory of Metallomics and Nanotechnology, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Pavel Kopel
- Department of Chemistry and Biochemistry, Laboratory of Metallomics and Nanotechnology, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Tomas Vaculovic
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Sona Krizkova
- Department of Chemistry and Biochemistry, Laboratory of Metallomics and Nanotechnology, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Marketa Vaculovicova
- Department of Chemistry and Biochemistry, Laboratory of Metallomics and Nanotechnology, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Laboratory of Metallomics and Nanotechnology, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Laboratory of Metallomics and Nanotechnology, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
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Lamley JM, Iuga D, Öster C, Sass HJ, Rogowski M, Oss A, Past J, Reinhold A, Grzesiek S, Samoson A, Lewandowski JR. Solid-State NMR of a Protein in a Precipitated Complex with a Full-Length Antibody. J Am Chem Soc 2014; 136:16800-6. [DOI: 10.1021/ja5069992] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jonathan M. Lamley
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Dinu Iuga
- Department
of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Carl Öster
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | | | - Marco Rogowski
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Andres Oss
- NMR
Institute and Tehnomeedikum, Tallinn University of Technology, Akadeemia
tee 15a, 19086 Tallinn, Estonia
| | - Jaan Past
- NMR
Institute and Tehnomeedikum, Tallinn University of Technology, Akadeemia
tee 15a, 19086 Tallinn, Estonia
| | - Andres Reinhold
- NMR
Institute and Tehnomeedikum, Tallinn University of Technology, Akadeemia
tee 15a, 19086 Tallinn, Estonia
| | | | - Ago Samoson
- NMR
Institute and Tehnomeedikum, Tallinn University of Technology, Akadeemia
tee 15a, 19086 Tallinn, Estonia
| | - Józef R. Lewandowski
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
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45
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Pickard FC, Miller BT, Schalk V, Lerner MG, Woodcock HL, Brooks BR. Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding. PLoS Comput Biol 2014; 10:e1003738. [PMID: 25058338 PMCID: PMC4109841 DOI: 10.1371/journal.pcbi.1003738] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A lesson utilizing a coarse-grained (CG) G-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org) to the Chemistry at HARvard Macromolecular Mechanics (CHARMM) molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the G-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG G model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field.
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Affiliation(s)
- Frank C. Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Benjamin T. Miller
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Vinushka Schalk
- Department of Natural Sciences, New College of Florida, Sarasota, Florida, United States of America
| | - Michael G. Lerner
- Department of Physics and Astronomy, Earlham College, Richmond, Indiana, United States of America
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida, United States of America
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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46
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Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model. Methods Mol Biol 2014; 1137:235-50. [PMID: 24573485 DOI: 10.1007/978-1-4939-0366-5_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Coarse-grained (CG) modeling is a well-acknowledged simulation approach for getting insight into long-time scale protein folding events at reasonable computational cost. Depending on the design of a CG model, the simulation protocols vary from highly case-specific-requiring user-defined assumptions about the folding scenario-to more sophisticated blind prediction methods for which only a protein sequence is required. Here we describe the framework protocol for the simulations of long-term dynamics of globular proteins, with the use of the CABS CG protein model and sequence data. The simulations can start from a random or a selected (e.g., native) structure. The described protocol has been validated using experimental data for protein folding model systems-the prediction results agreed well with the experimental results.
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47
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Lewandowski JR. Advances in solid-state relaxation methodology for probing site-specific protein dynamics. Acc Chem Res 2013; 46:2018-27. [PMID: 23621579 DOI: 10.1021/ar300334g] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Dynamics are intimately linked to protein stability and play a crucial role in important biological processes, such as ligand binding, allosteric regulation, protein folding, signaling, and enzymatic catalysis. Solid-state NMR relaxation measurements allow researchers to determine the amplitudes, time scales, and under favorable conditions, directionality of motions at atomic resolution over the entire range of dynamic processes from picoseconds to milliseconds. Because this method allows researchers to examine both the amplitudes and time scales of motions in this range, they can link different tiers of protein motions in protein energy landscapes. As a result, scientists can better understand the relationships between protein motions and functions. Such studies are possible both with the primary targets of solid-state NMR studies, such as amyloid fibrils, membrane proteins, or other heterogeneous systems, and others that researchers typically study by solution NMR and X-ray crystallography. In addition, solid-state NMR, with the absence of tumbling in solution, eliminates the intrinsic size limitation imposed by slow tumbling of large proteins. Thus, this technique allows researchers to characterize interdomain and intermolecular interactions in large complexes at the atomic scale. In this Account, we discuss recent advances in solid-state relaxation methodology for studying widespread site-specific protein dynamics. We focus on applications involving magic angle spinning, one of the primary methods used in high-resolution solid-state NMR. We give an overview of challenges and solutions for measuring (15)N and (13)C spin-lattice relaxation (R1) to characterize fast picosecond-nanosecond motions, spin-lattice in the rotating frame (R1ρ), and other related relaxation rates for characterization of picosecond-millisecond protein motions. In particular, we discuss the problem of separating incoherent effects caused by random motions from coherent effects arising from incomplete averaging of orientation-dependent NMR interactions. We mention a number of quantitative studies of protein dynamics based on solid-state relaxation measurements. Finally, we discuss the potential use of relaxation measurements for extracting the directionality of motions. Using the (15)N and (13)C R1 and R1ρ measurements, we illustrate the backbone and side-chain dynamics in the protein GB1 and comment on this emerging dynamic picture within the context of data from solution NMR measurements and simulations.
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Blaszczyk M, Jamroz M, Kmiecik S, Kolinski A. CABS-fold: Server for the de novo and consensus-based prediction of protein structure. Nucleic Acids Res 2013; 41:W406-11. [PMID: 23748950 PMCID: PMC3692050 DOI: 10.1093/nar/gkt462] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competitions as one of the leading approaches for de novo and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The web server output is a coarse-grained trajectory of generated conformations, its Jmol representation and predicted models in all-atom resolution (together with accompanying analysis). CABS-fold can be freely accessed at http://biocomp.chem.uw.edu.pl/CABSfold.
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Affiliation(s)
- Maciej Blaszczyk
- Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics. Int J Mol Sci 2013; 14:9893-905. [PMID: 23665897 PMCID: PMC3676820 DOI: 10.3390/ijms14059893] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/09/2013] [Accepted: 04/24/2013] [Indexed: 01/30/2023] Open
Abstract
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
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50
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Jamroz M, Orozco M, Kolinski A, Kmiecik S. Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field. J Chem Theory Comput 2012; 9:119-25. [PMID: 26589015 DOI: 10.1021/ct300854w] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.
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Affiliation(s)
- Michal Jamroz
- Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Modesto Orozco
- IRB - BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine , Josep Samitier 1-5, Barcelona 08028, Spain.,Department of Biochemistry, Universitat of Barcelona , Gran Via de les Corts Catalanes, 585 08007 Barcelona, Spain
| | - Andrzej Kolinski
- Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Sebastian Kmiecik
- Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
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