1
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Krupa MA, Krupa P. Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking. Methods Mol Biol 2024; 2780:27-41. [PMID: 38987462 DOI: 10.1007/978-1-0716-3985-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Docking methods can be used to predict the orientations of two or more molecules with respect of each other using a plethora of various algorithms, which can be based on the physics of interactions or can use information from databases and templates. The usability of these approaches depends on the type and size of the molecules, whose relative orientation will be estimated. The two most important limitations are (i) the computational cost of the prediction and (ii) the availability of the structural information for similar complexes. In general, if there is enough information about similar systems, knowledge-based and template-based methods can significantly reduce the computational cost while providing high accuracy of the prediction. However, if the information about the system topology and interactions between its partners is scarce, physics-based methods are more reliable or even the only choice. In this chapter, knowledge-, template-, and physics-based methods will be compared and briefly discussed providing examples of their usability with a special emphasis on physics-based protein-protein, protein-peptide, and protein-fullerene docking in the UNRES coarse-grained model.
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Affiliation(s)
- Magdalena A Krupa
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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2
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Sieradzan AK, Sans-Duñó J, Lubecka EA, Czaplewski C, Lipska AG, Leszczyński H, Ocetkiewicz KM, Proficz J, Czarnul P, Krawczyk H, Liwo A. Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins. J Comput Chem 2023; 44:602-625. [PMID: 36378078 DOI: 10.1002/jcc.27026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/19/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022]
Abstract
We report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms to minimize the number of operations and to improve numerical stability, (iv) using OpenMP to parallelize those sections of the code for which distributed-memory parallelization involves unfavorable computing/communication time ratio, and (v) careful memory management to minimize simultaneous access of distant memory sections. The new code enables us to run molecular dynamics simulations of protein systems with size exceeding 100,000 amino-acid residues, reaching over 1 ns/day (1 μs/day in all-atom timescale) with 24 cores for proteins of this size. Parallel performance of the code and comparison of its performance with that of AMBER, GROMACS and MARTINI 3 is presented.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Jordi Sans-Duñó
- Department of Chemistry, University of Lleida, Lleida, Spain
| | - Emilia A Lubecka
- Faculty of Electronics, Telecommunication and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Henryk Leszczyński
- Faculty of Mathematics, Physics and Informatics, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Krzysztof M Ocetkiewicz
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Jerzy Proficz
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Paweł Czarnul
- Faculty of Electronics, Telecommunication and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Henryk Krawczyk
- Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Faculty of Electronics, Telecommunication and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.,Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland
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3
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Bojko M, Węgrzyn K, Sikorska E, Kocikowski M, Parys M, Battin C, Steinberger P, Kogut MM, Winnicki M, Sieradzan AK, Spodzieja M, Rodziewicz-Motowidło S. Design, synthesis and biological evaluation of PD-1 derived peptides as inhibitors of PD-1/PD-L1 complex formation for cancer therapy. Bioorg Chem 2022; 128:106047. [DOI: 10.1016/j.bioorg.2022.106047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/04/2022] [Accepted: 07/19/2022] [Indexed: 12/11/2022]
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4
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Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins. J Mol Model 2022; 28:201. [PMID: 35748949 DOI: 10.1007/s00894-022-05154-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 10/17/2022]
Abstract
Metal ions play important biological roles, e.g., activation or deactivation of enzymatic reactions and signal transduction. Moreover, they can stabilize protein structure, or even be actively involved in the protein folding process. Therefore, accurate treatment of the ions is crucial to model and investigate biological phenomena properly. In this work the coarse-grained UNRES (UNited RESidue) force field was extended to include the interactions between proteins and four alkali or alkaline earth metal cations of biological significance, i.e., calcium, magnesium, sodium and potassium. Additionally, chloride anions were introduced as counter-ions. Parameters were derived from all-atom simulations and incorporate water in an implicit manner. The new force field was tested on the set of the proteins and was able to reproduce the ion-binding preferences.
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5
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2376:399-416. [PMID: 34845623 DOI: 10.1007/978-1-0716-1716-8_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics and its replica-exchange extensions, UNRES has found a variety of applications, including ab initio and database-assisted protein-structure prediction, simulating protein-folding pathways, exploring protein free-energy landscapes, and solving biological problems. This chapter provides a summary of UNRES and a guide for potential users regarding the application of the UNRES package in a variety of research tasks.
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6
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Rojas AV, Maisuradze GG, Scheraga HA, Liwo A. Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field. Methods Mol Biol 2022; 2340:79-104. [PMID: 35167071 DOI: 10.1007/978-1-0716-1546-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation is the cause of many, often lethal, diseases, including the Alzheimer's, Parkinson's, and Huntington's diseases, and familial amyloidosis. Theoretical investigation of the mechanism of this process, including the structures of the oligomeric intermediates which are the most toxic, is difficult because of long time scale of aggregation. Coarse-grained models, which enable us to extend the simulation time scale by three or more orders of magnitude, are, therefore, of great advantage in such studies. In this chapter, we describe the application of the physics-based UNited RESidue (UNRES) force field developed in our laboratory to study protein aggregation, in both free simulations and simulations of aggregation propagation from an existing template (seed), and illustrate it with the examples of Aβ-peptide aggregation and Aβ-peptide-assisted aggregation of the peptides derived from the repeat domains of tau (TauRD).
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Affiliation(s)
- Ana V Rojas
- Schrodinger Inc., 120 West 45th Street New York, New York, 10036, NY, USA
| | - Gia G Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, 14853-1301, NY, USA
| | - Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, 14853-1301, NY, USA
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.
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7
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Krupa P, Karczyńska AS, Mozolewska MA, Liwo A, Czaplewski C. UNRES-Dock-protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations. Bioinformatics 2021; 37:1613-1615. [PMID: 33079977 DOI: 10.1093/bioinformatics/btaa897] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 09/04/2020] [Accepted: 10/06/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. Although there are many tools to predict the structures of single-chain proteins or protein complexes with small ligands, peptide-protein and protein-protein docking is more challenging. In this work, we utilized multiplexed replica-exchange molecular dynamics (MREMD) simulations with the physics-based heavily coarse-grained UNRES model, which provides more than a 1000-fold simulation speed-up compared with all-atom approaches to predict structures of protein complexes. RESULTS We present a new protein-protein and peptide-protein docking functionality of the UNRES package, which includes a variable degree of conformational flexibility. UNRES-Dock protocol was tested on a set of 55 complexes with size from 43 to 587 amino-acid residues, showing that structures of the complexes can be predicted with good quality, if the sampling of the conformational space is sufficient, especially for flexible peptide-protein systems. The developed automatized protocol has been implemented in the standalone UNRES package and in the UNRES server. AVAILABILITY AND IMPLEMENTATION UNRES server: http://unres-server.chem.ug.edu.pl; UNRES package and data used in testing of UNRES-Dock: http://unres.pl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Paweł Krupa
- Faculty of Chemistry, University of Gdańsk, Gdańsk 80-308, Poland.,Institute of Physics, Polish Academy of Sciences, Warsaw 02-668, Poland
| | - Agnieszka S Karczyńska
- Faculty of Chemistry, University of Gdańsk, Gdańsk 80-308, Poland.,University of Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble 38000, France
| | | | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk 80-308, Poland
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8
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Krupa P, Spodzieja M, Sieradzan AK. Prediction of CD28-CD86 protein complex structure using different level of resolution approach. J Mol Graph Model 2020; 103:107802. [PMID: 33246194 DOI: 10.1016/j.jmgm.2020.107802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/29/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022]
Abstract
Immune system plays essential role in functioning of higher organisms. Its hyperactivity can lead to autoimmune diseases or even anaphylactic shock while hypoactivity leads to proneness to infections or even cancer. T-cells play crucial role in immunity mechanisms and their activation and inhibition is strictly controlled by the regulatory proteins, such as CD28 and CTLA-4. Activity of these proteins is controlled by a pair of ligands, named CD80 and CD86, which can non-covalently bound to their receptors. While structure of human CTLA-4-CD86 complex in known, there is still no available structure for the CD28-CD86 system. To obtain the reliable structure of CD28-CD86 complex we first validated our methodology on the CTLA-4-CD86 system. Then coarse-grained UNRES-dock molecular docking simulation was performed followed by all-atom molecular dynamics simulations. As a result, we obtained a complete CD28-CD86 complex structure on atomistic level, in which interaction interface is consistent with available data. We also determined the kinetic properties for CTLA4-CD86 and CD28-CD86 complexes with use of coarse-grained model and determined the key residues for complex formation with use of Robetta, PPCheck and HawkDock servers. Our results not only verify high accuracy of the UNRES-dock method, but also provide a highly reliable model of the CD28-CD86 complex, which can be used in further studies and drug design.
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Affiliation(s)
- Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Marta Spodzieja
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
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9
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Spodzieja M, Kuncewicz K, Sieradzan A, Karczyńska A, Iwaszkiewicz J, Cesson V, Węgrzyn K, Zhukov I, Maszota-Zieleniak M, Michielin O, Speiser DE, Zoete V, Derré L, Rodziewicz-Motowidło S. Disulfide-Linked Peptides for Blocking BTLA/HVEM Binding. Int J Mol Sci 2020; 21:ijms21020636. [PMID: 31963646 PMCID: PMC7013932 DOI: 10.3390/ijms21020636] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 12/26/2022] Open
Abstract
Immune checkpoints are crucial in the maintenance of antitumor immune responses. The activation or blockade of immune checkpoints is dependent on the interactions between receptors and ligands; such interactions can provide inhibitory or stimulatory signals, including the enhancement or suppression of T-cell proliferation, differentiation, and/or cytokine secretion. B-and T-lymphocyte attenuator (BTLA) is a lymphoid-specific cell surface receptor which is present on T-cells and interacts with herpes virus entry mediator (HVEM), which is present on tumor cells. The binding of HVEM to BTLA triggers an inhibitory signal which attenuates the immune response. This feature is interesting for studying the molecular interactions between HVEM and BTLA, as they may be targeted for novel immunotherapies. This work was based on the crystal structure of the BTLA/HVEM complex showing that BTLA binds the N-terminal cysteine-rich domain of HVEM. We investigated the amino acid sequence of HVEM and used molecular modeling methods to develop inhibitors of the BTLA/HVEM interaction. We synthesized novel compounds and determined their ability to interact with the BTLA protein and inhibit the formation of the BTLA/HVEM complex. Our results suggest that the HVEM (14-39) peptide is a potent inhibitor of the formation of the BTLA/HVEM protein complex.
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Affiliation(s)
- Marta Spodzieja
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80–308 Gdańsk, Poland; (M.S.); (K.K.); (A.S.); (A.K.); (M.M.-Z.)
| | - Katarzyna Kuncewicz
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80–308 Gdańsk, Poland; (M.S.); (K.K.); (A.S.); (A.K.); (M.M.-Z.)
| | - Adam Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80–308 Gdańsk, Poland; (M.S.); (K.K.); (A.S.); (A.K.); (M.M.-Z.)
| | - Agnieszka Karczyńska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80–308 Gdańsk, Poland; (M.S.); (K.K.); (A.S.); (A.K.); (M.M.-Z.)
| | - Justyna Iwaszkiewicz
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipole, CH-1015 Lausanne, Switzerland; (J.I.); (O.M.); (V.Z.)
| | - Valérie Cesson
- Urology Research Unit, Urology Department, University Hospital of Lausanne (CHUV), CH-1011 Lausanne, Switzerland;
| | - Katarzyna Węgrzyn
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdansk, Abrahama 58, 80–308 Gdańsk, Poland;
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02–106 Warszawa, Poland;
- NanoBioMedical Center, Adam Mickiewicz University, Umultowska 85, 61–614 Poznań, Poland
| | - Martyna Maszota-Zieleniak
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80–308 Gdańsk, Poland; (M.S.); (K.K.); (A.S.); (A.K.); (M.M.-Z.)
| | - Olivier Michielin
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipole, CH-1015 Lausanne, Switzerland; (J.I.); (O.M.); (V.Z.)
- Department of Oncology, University Hospital of Lausanne (CHUV), Ludwig Cancer Research—Lausanne Branch, CH-1011 Lausanne, Switzerland
| | - Daniel E. Speiser
- Department of Oncology, University of Lausanne, Ch. des Boveresses 155, CH-1066 Lausanne, Switzerland;
| | - Vincent Zoete
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipole, CH-1015 Lausanne, Switzerland; (J.I.); (O.M.); (V.Z.)
- Department of Fundamental Oncology, Lausanne University, Ludwig Institute for Cancer Research, Route de la Corniche 9A, CH-1066 Epalinges, Switzerland
| | - Laurent Derré
- Urology Research Unit, Urology Department, University Hospital of Lausanne (CHUV), CH-1011 Lausanne, Switzerland;
- Correspondence: (L.D.); (S.R.-M.)
| | - Sylwia Rodziewicz-Motowidło
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80–308 Gdańsk, Poland; (M.S.); (K.K.); (A.S.); (A.K.); (M.M.-Z.)
- Correspondence: (L.D.); (S.R.-M.)
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10
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Ziȩba K, Ślusarz M, Ślusarz R, Liwo A, Czaplewski C, Sieradzan AK. Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer. J Phys Chem B 2019; 123:7829-7839. [PMID: 31454484 DOI: 10.1021/acs.jpcb.9b06700] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The physics-based UNRES coarse-grained force field for the simulations of protein structure and dynamics has been extended to treat membrane proteins. The lipid bilayer has been modeled by introducing a continuous nonpolar phase with the water-interface region of appropriate thickness. The potentials for average electrostatic and correlation interactions of the peptide groups have been rescaled to account for the reduction of the dielectric permittivity compared to the water phase and new potentials for protein side-chain-side-chain interactions inside and across the lipid phase have been introduced. The model was implemented in the UNRES package for coarse-grained simulations of proteins, and the package with the new functionality was tested for total energy conservation and thermostat behavior in microcanonical and canonical molecular dynamics simulations runs, respectively. The method was validated by running unrestricted ab initio blind-prediction tests of 10 short α-helical membrane proteins, all runs started from the extended structures. The modified UNRES force field was able to predict correctly the overall folds of the membrane proteins studied.
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Affiliation(s)
- Karolina Ziȩba
- Faculty of Chemistry , University of Gdańsk , Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Magdalena Ślusarz
- Faculty of Chemistry , University of Gdańsk , Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Rafał Ślusarz
- 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
| | - Cezary Czaplewski
- Faculty of Chemistry , University of Gdańsk , Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Adam K Sieradzan
- Faculty of Chemistry , University of Gdańsk , Wita Stwosza 63 , 80-308 Gdańsk , Poland
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11
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Nguyen HL, Krupa P, Hai NM, Linh HQ, Li MS. Structure and Physicochemical Properties of the Aβ42 Tetramer: Multiscale Molecular Dynamics Simulations. J Phys Chem B 2019; 123:7253-7269. [DOI: 10.1021/acs.jpcb.9b04208] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hoang Linh Nguyen
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software
City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Biomedical Engineering Department, Ho Chi Minh City University of Technology-VNU HCM, 268 Ly Thuong Kiet Street, Distr. 10, Ho Chi Minh City 700000, Vietnam
| | - Pawel Krupa
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Nguyen Minh Hai
- Faculty of Physics and Engineering Physics, University of Science-VNU HCM, Ho Chi Minh City 700000, Vietnam
| | - Huynh Quang Linh
- Biomedical Engineering Department, Ho Chi Minh City University of Technology-VNU HCM, 268 Ly Thuong Kiet Street, Distr. 10, Ho Chi Minh City 700000, Vietnam
| | - Mai Suan Li
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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12
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Faraggi E, Krupa P, Mozolewska MA, Liwo A, Kloczkowski A. Reoptimized UNRES Potential for Protein Model Quality Assessment. Genes (Basel) 2018; 9:genes9120601. [PMID: 30513992 PMCID: PMC6315818 DOI: 10.3390/genes9120601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/25/2018] [Accepted: 11/27/2018] [Indexed: 11/16/2022] Open
Abstract
Ranking protein structure models is an elusive problem in bioinformatics. These models are evaluated on both the degree of similarity to the native structure and the folding pathway. Here, we simulated the use of the coarse-grained UNited RESidue (UNRES) force field as a tool to choose the best protein structure models for a given protein sequence among a pool of candidate models, using server data from the CASP11 experiment. Because the original UNRES was optimized for Molecular Dynamics simulations, we reoptimized UNRES using a deep feed-forward neural network, and we show that introducing additional descriptive features can produce better results. Overall, we found that the reoptimized UNRES performs better in selecting the best structures and tracking protein unwinding from its native state. We also found a relatively poor correlation between UNRES values and the model’s Template Modeling Score (TMS). This is remedied by reoptimization. We discuss some cases where our reoptimization procedure is useful.
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Affiliation(s)
- Eshel Faraggi
- Research and Information Systems, LLC, Indianapolis, IN 46240, USA.
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH 43215, USA.
| | - Pawel Krupa
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH 43215, USA.
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, PL-02-668 Warsaw, Poland.
| | - Magdalena A Mozolewska
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH 43215, USA.
- Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, 01-248 Warszawa, 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, Korea.
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH 43215, USA.
- Department of Pediatrics, The Ohio State University, Columbus, OH 43215, USA.
- Kavli Institute for Theoretical Physics China, Chinese Academy of Sciences, Beijing 100190, China.
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13
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Sieradzan AK, Giełdoń A, Yin Y, He Y, Scheraga HA, Liwo A. A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. J Comput Chem 2018; 39:2360-2370. [PMID: 30306573 PMCID: PMC6487257 DOI: 10.1002/jcc.25571] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/29/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
Abstract
Based on the coarse-grained UNRES and NARES-2P models of proteins and nucleic acids, respectively, developed in our laboratory, in this work we have developed a coarse-grained model of systems containing proteins and nucleic acids. The UNRES and NARES-2P effective energy functions have been applied to the protein and nucleic-acid components of a system, respectively, while protein-nucleic-acid interactions have been described by the respective coarse-grained potentials developed in our recent work (Yin et al., J. Chem Theory Comput. 2015, 11, 1792). The Debye-Hückel screening has been applied to the electrostatic-interaction energy between the phosphate groups and charged amino-acid side chains. The model has been integrated into the UNRES package for coarse-grained molecular dynamics simulations of proteins and the implementation has been tested for energy conservation in microcanonical molecular dynamics runs and for temperature conservation in canonical molecular dynamics runs. Two case studies were performed: (i) the dynamics of the Ku protein heterodimer bound to DNA, for which it was found that the Ku70/Ku80 protein complex plays an active role in DNA repairing and (ii) conformational changes of the multiple antibiotic resistance (MarA) protein occurring during DNA binding, for which the functionally important motions occurring during this process were identified. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Yanping Yin
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853-1301, U.S.A
| | - Yi He
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853-1301, U.S.A
- School of Engineering, University of California Merced, 5200 N. Lake Road, Merced, CA 95343, U.S.A
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853-1301, U.S.A
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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Sieradzan AK, Mozolewska MA. Extension of coarse-grained UNRES force field to treat carbon nanotubes. J Mol Model 2018; 24:121. [PMID: 29700628 PMCID: PMC5920012 DOI: 10.1007/s00894-018-3656-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/13/2018] [Indexed: 11/25/2022]
Abstract
Carbon nanotubes (CNTs) have recently received considerable attention because of their possible applications in various branches of nanotechnology. For their cogent application, knowledge of their interactions with biological macromolecules, especially proteins, is essential and computer simulations are very useful for such studies. Classical all-atom force fields limit simulation time scale and size of the systems significantly. Therefore, in this work, we implemented CNTs into the coarse-grained UNited RESidue (UNRES) force field. A CNT is represented as a rigid infinite-length cylinder which interacts with a protein through the Kihara potential. Energy conservation in microcanonical coarse-grained molecular dynamics simulations and temperature conservation in canonical simulations with UNRES containing the CNT component have been verified. Subsequently, studies of three proteins, bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTs, were performed to examine the influence of CNTs on the structure and dynamics of these proteins. It was found that nanotubes bind to these proteins and influence their structure. Our results show that the UNRES force field can be used for further studies of CNT-protein systems with 3-4 order of magnitude larger timescale than using regular all-atom force fields. Graphical abstract Bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTsᅟ.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Magdalena A Mozolewska
- Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308, Gdansk, Poland.
- Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, 01-248, Warsaw, Poland.
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15
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Sieradzan AK, Jakubowski R. Introduction of steered molecular dynamics into UNRES coarse-grained simulations package. J Comput Chem 2017; 38:553-562. [DOI: 10.1002/jcc.24685] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/08/2016] [Accepted: 11/09/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Adam K. Sieradzan
- Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 Gdańsk 80-308 Poland
| | - Rafał Jakubowski
- Faculty of Physics, Astronomy and Informatics, Institute of Physics, Nicolaus Copernicus University; Grudziadzka 5 Torun 87-100 Poland
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16
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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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17
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Tachikawa H, Takada T. Ionization dynamics of the branched water cluster: A long-lived non-proton-transferred intermediate. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Zaborowski B, Jagieła D, Czaplewski C, Hałabis A, Lewandowska A, Żmudzińska W, Ołdziej S, Karczyńska A, Omieczynski C, Wirecki T, Liwo A. A Maximum-Likelihood Approach to Force-Field Calibration. J Chem Inf Model 2015; 55:2050-70. [DOI: 10.1021/acs.jcim.5b00395] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Bartłomiej Zaborowski
- Faculty
of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Dawid Jagieła
- Faculty
of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Cezary Czaplewski
- Faculty
of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Anna Hałabis
- Laboratory
of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki
24, 80-922 Gdańsk, Poland
| | - Agnieszka Lewandowska
- Laboratory
of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki
24, 80-922 Gdańsk, Poland
| | - Wioletta Żmudzińska
- Laboratory
of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki
24, 80-922 Gdańsk, Poland
| | - Stanisław Ołdziej
- Laboratory
of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki
24, 80-922 Gdańsk, Poland
| | - Agnieszka Karczyńska
- Faculty
of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Christian Omieczynski
- Faculty
of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Tomasz Wirecki
- Faculty
of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam Liwo
- Faculty
of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
- Center
for In Silico Protein Structure and School of Computational Sciences, Korea Institute for Advanced Study, 87 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
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19
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Lipska AG, Sieradzan AK, Krupa P, Mozolewska MA, D’Auria S, Liwo A. Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field. J Mol Model 2015; 21:64. [DOI: 10.1007/s00894-015-2609-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/08/2015] [Indexed: 11/30/2022]
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