Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.
Coarse graining
Molecular dynamics simulations
Protein dynamics
Protein folding
Protein–structure prediction
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2022
2022
Historique:
entrez:
30
11
2021
pubmed:
1
12
2021
medline:
19
1
2022
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 34845623
doi: 10.1007/978-1-0716-1716-8_23
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
399-416Informations de copyright
© 2022. Springer Science+Business Media, LLC, part of Springer Nature.
Références
Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A (2016) Coarse-grained protein models and their applications. Chem Rev 116:7898–7936
pubmed: 27333362
Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink S-J (2008) The MARTINI coarse-grained force field: extension to proteins. J Chem Theory Comput 4:819–834
pubmed: 26621095
Liwo A, Czaplewski C, Oldziej S, Rojas AV, Kazmierkiewicz R, Makowski M, Murarka RK, Scheraga HA (2008) Simulation of protein structure and dynamics with the coarse-grained UNRES force field. In: Voth G (ed) Coarse-graining of condensed phase and biomolecular systems. Taylor & Francis, Oxfordshire, pp 107–122
Liwo A, Baranowski M, Czaplewski C, Golas E, He Y, Jagiela D, Krupa P, Maciejczyk M, Makowski M, Mozolewska MA, Niadzvedtski A, Oldziej S, Scheraga HA, Sieradzan AK, Slusarz R, Wirecki T, Yin Y, Zaborowski B (2014) A unified coarse-grained model of biological macromolecules based on mean-field multipole.Multipole interactions. J Mol Model 20:2306
Kubo R (1962) Generalized cumulant expansion method. J Phys Soc Jpn 17:1100–1120
Liwo A, Czaplewski C, Pillardy J, Scheraga HA (2001) Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field. J Chem Phys 115:2323–2347
Sieradzan AK, Makowski M, Augustynowicz A, Liwo A (2017) A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains. J Chem Phys 146:124106
pubmed: 28388107
He Y, Mozolewska M, Krupa P, Sieradzan AK, Wirecki TK, Liwo A, Kachlishvili K, Rackovsky S, Jagiela D, Slusarz R, Czaplewski CR, Oldziej S, Scheraga HA (2013) Lessons from application of the UNRES force field to predictions of structures of CASP10 targets. Proc Natl Acad Sci U S A 110:14936–14941
pubmed: 23980156
pmcid: 3773777
Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, Wirecki T, Cooper S, Flatten J, Xu F, Baker D, Cheng J, Delbem ACB, Floudas CA, Keasar C, Levitt M, Popovic Z, Scheraga HA, Skolnick J, Crivelli SN, Players F (2014) WeFold: a coopetition for protein structure prediction. Proteins 82:1850–1868
pubmed: 24677212
pmcid: 4249725
Krupa P, Mozolewska MA, Wiśniewska M, Yin Y, He Y, Sieradzan AK, Ganzynkowicz R, Lipska AG, Karczynska A, Slusarz M, Slusarz R, Gieldon A, Czaplewski C, Jagiela D, Zaborowski B, Scheraga HA, Liwo A (2016) Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinformatics 32:3270–3278
Karczynska AS, Mozolewska MA, Krupa P, Gieldon A, Liwo A, Czaplewski C (2018) Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information. Proteins 86(S1):228–239
pubmed: 29134679
Lubecka EA, Karczynska AS, Lipska AG, Sieradzan AK, Zieba K, Sikorska C, Uciechowska U, Samsonov SA, Krupa P, Mozolewska MA, Golon L, Gieldon A, Czaplewski C, Slusarz R, Slusarz M, Crivelli SN, Liwo A (2019) Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment. J Mol Graph Model 92:154–166
pubmed: 31376733
Karczynska A, Zieba K, Uciechowska U, Mozolewska MA, Krupa P, Lubecka EA, Lipska AG, Sikorska C, Samsonov SA, Sieradzan AK, Gieldon A, Liwo A, Slusarz R, Slusarz M, Lee J, Joo K, Czaplewski C (2020) Improved consensus-fragment selection in template-assisted prediction of protein structures with the UNRES force field in CASP13. J Chem Inf Model 60:1844–1864
pubmed: 31999919
pmcid: 7588044
Liwo A, Khalili M, Scheraga HA (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc Natl Acad Sci U S A 102:2362–2367
pubmed: 15677316
pmcid: 548970
Maisuradze GG, Senet P, Czaplewski C, Liwo A, Scheraga HA (2010) Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A 114:4471–4485
pubmed: 20166738
pmcid: 2849147
Zhou R, Maisuradze GG, Sunol D, Todorovski T, Macias MJ, Xiao Y, Scheraga HA, Czaplewski C, Liwo A (2014) Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements. Proc Natl Acad Sci U S A 2014(111):18243–18248
Lipska AG, Seidman SR, Sieradzan AK, Gieldon A, Liwo A, Scheraga HA (2016) Molecular dynamics of protein a and a WW domain with a united-residue model including hydrodynamic interaction. J Chem Phys 144:184110
pubmed: 27179474
pmcid: 4866947
Krupa P, Sieradzan AK, Mozolewska MA, Li H, Liwo A, Scheraga HA (2017) Dynamics of disulfide-bond disruption and formation in the thermal unfolding of ribonuclease A. J Chem Theory Comput 13:5721–5730
pubmed: 28942648
Rojas A, Liwo A, Browne D, Scheraga HA (2010) Mechanism of fiber assembly; treatment of A β-peptide aggregation with a coarse-grained united-residue force field. J Mol Biol 404:537–552
pubmed: 20888834
pmcid: 2981693
He Y, Liwo A, Weinstein H, Scheraga HA (2011) PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. J Mol Biol 405:298–314
pubmed: 21050858
Golas E, Maisuradze GG, Senet P, Oldziej S, Czaplewski C, Scheraga HA, Liwo A (2012) Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. J Chem Theory Comput 8:1750–1764
pubmed: 22737044
pmcid: 3380372
Mozolewska M, Krupa P, Scheraga HA, Liwo A (2015) Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches. Proteins 83:1414–1426
pubmed: 25973573
pmcid: 4509829
Rojas AV, Liwo A, Scheraga HA (2007) Molecular dynamics with the united-residue force field: ab initio folding simulations of multichain proteins. J Phys Chem B 111:293–309
pubmed: 17201452
pmcid: 2597722
Sieradzan AK (2015) Introduction of periodic boundary conditions into UNRES force field. J Comput Chem 36:940–946
pubmed: 25753584
Kozlowska U, Maisuradze GG, Liwo A, Scheraga HA (2010) Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. 2. Results, comparison with statistical potentials, and implementation in the UNRES force field. J Comput Chem 31:1154–1167
pubmed: 20017135
pmcid: 2849738
Sieradzan AK, Niadzvedtski A, Scheraga HA, Liwo A (2014) Revised backbone-virtual-bond-angle potentials to treat the L- and D-amino-acid residues in the coarse-grained united residue (UNRES) force field. J Chem Theory Comput 10:2194–2203
pubmed: 24839411
pmcid: 4020588
Liwo A, Oldziej S, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA (1997) A united-residue force field for off-lattice protein-structure simulations. I: Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. I: Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. J Comput Chem 18:849–873
Makowski M, Liwo A, Scheraga HA (2017) 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 121:379–390
pubmed: 28000446
Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA (1993) Prediction of protein conformation on the basis of a search for compact structures; test on avian pancreatic polypeptide. Prot Sci 2:1715–1731
Sieradzan AK, Hansmann UHE, Scheraga HA, Liwo A (2012) Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. J Chem Theory Comput 8:4746–4757
pubmed: 24729761
pmcid: 3982868
Sieradzan AK, Krupa P, Scheraga HA, Liwo A, Czaplewski C (2015) Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the united residue (UNRES) force field for protein simulations. J Chem Theory Comput 11:817–831
pubmed: 25691834
pmcid: 4327884
Liwo A, Oldziej S, Czaplewski C, Kozlowska U, Scheraga HA (2004) Parameterization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems. J Phys Chem B 108:9421–9438
Liwo A, Khalili M, Czaplewski C, Kalinowski S, Oldziej S, Wachucik K, Scheraga HA (2007) Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins. J Phys Chem B 111:260–285
pubmed: 17201450
pmcid: 3236617
Chinchio M, Czaplewski C, Liwo A, Oldziej S, Scheraga HA (2007) Dynamic formation and breaking of disulfide bonds in molecular dynamics simulations with the UNRES force field. J Chem Theory Comput 3:1236–1248
pubmed: 26633198
Krupa P, Halabis A, Zmudzinska W, Oldziej S, Scheraga HA, Liwo A (2017) Maximum likelihood calibration of the UNRES force field for simulation of protein structure and dynamics. J Chem Inf Model 57:2364–2377
pubmed: 28809487
Liwo A, Sieradzan AK, Lipska AG, Czaplewski C, Joung I, Zmudzinska W, Halabis A, Oldziej S (2019) A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation. J Chem Phys 150:155104
Sieradzan AK, Lipska AG, Lubecka EA (2017) Shielding effect in protein folding. J Mol Graph Model 79:118–132
Sieradzan AK, Mozolewska M (2018) Extension of coarse-grained UNRES force field to treat carbon nanotubes. J Mol Model 24:121
pubmed: 29700628
pmcid: 5920012
Zieba K, Slusarz M, Slusarz R, Liwo A, Czaplewski C, Sieradzan AK (2019) Extension of the UNRES coarse-grained force field to membrane proteins in the lipid bilayer. J Phys Chem B 123:7829–7839
pubmed: 31454484
Sieradzan AK, Bogunia M, Mech P, Ganzynkowicz R, Gieldon A, Liwo A, Makowski M (2019) Introduction of phosphorylated residues into the UNRES coarse-grained model: toward modeling of signaling processes. J Phys Chem B 23:5721–5729
Gay DM (1983) Algorithm 611. Subroutines for unconstrained minimization using a model/trust-region approach. ACM Trans Math Software 9:503–524
Khalili M, Liwo A, Jagielska A, Scheraga HA (2005) Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model α-helical systems. J Phys Chem B 109:13798–13810
pubmed: 16852728
pmcid: 2564622
Kleinerman DS, Czaplewski C, Liwo A, Scheraga HA (2008) Implementations of Nose-Hoover and Nose-Poincare termostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain. J Chem Phys 128:245103
Lee J, Scheraga HA, Rackovsky S (1998) Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. Biopolymers 46:103–116
Hansmann UHE, Okamoto Y (1994) Comparative study of multicanonical algorithm and multicanonical replica exchange method for simulating systems with rough energy landscape. Physica A 212:415–437
Rhee YM, Pande VS (2003) Multiplexed replica exchange molecular dynamics method for protein folding simulations. Biophys J 84:775–786
pubmed: 12547762
pmcid: 1302658
Czaplewski C, Kalinowski S, Liwo A, Scheraga HA (2009) Application of multiplexed replica exchange molecular dynamics to the UNRES force field: tests with α and α+β proteins. J Chem Theor Comput 5:627–640
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM (1992) The weighted histogram analysis method for free energy calculations on biomolecules. I. The method. J Comput Chem 13:1011–1021
McGuffin L, Bryson K, Jones D (2000) The PSIPRED protein structure prediction server. Bioinformatics 16:404–405
pubmed: 10869041
Sieradzan AK, Jakubowski R (2017) Introduction of steered molecular dynamics into UNRES coarse-grained simulations package. J Comput Chem 38:553–562
pubmed: 28074486
Lubecka EA, Liwo A (2019) Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints. J Comput Chem 40:2164–2178
Mozolewska MA, Krupa P, Zaborowski B, Liwo A, Lee J, Joo K, Czaplewski C (2016) 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 56:2263–2279
pubmed: 27749055
Karczynska AS, Czaplewski C, Krupa P, Mozolewska MA, Joo K, Lee J, Liwo A (2017) Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins. J Comput Chem 38:2730–2746
pubmed: 28940211
Fajardo JE, Shrestha R, Gil N, Belsom A, Crivelli SN, Czaplewski C, Fidelis C, Grudinin S, Karasikov M, Karczynska AS, Kryshtafovych A, Leitner A, Liwo A, Lubecka EA, Monastyrskyy B, Pages G, Rappsilber J, Sieradzan AK, Sikorska C, Trabjerg E, Fiser A (2019) Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. Proteins 87:1283–1297
pubmed: 31569265
pmcid: 6851497
Murtagh F (1985) Multidimensional clustering algorithms. Springer Verlag, Vienna
Rotkiewicz P, Skolnick J (2008) Fast procedure for reconstruction of full-atom protein models from reduced representations. J Comput Chem 29:1460–1465
pubmed: 18196502
pmcid: 2692024
Wang Q, Canutescu AA, Dunbrack RL (2008) SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. Nat Protoc 3:1832–1847
pubmed: 18989261
pmcid: 2682191
Lubecka EA, Liwo A (2016) New UNRES force field package with FORTRAN 90. TASK Quart 20:399–407
Liwo A, Oldziej S, Czaplewski C, Kleinerman DS, Blood P, Scheraga HA (2010) Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics. J ChemTheory Comput 6:890–909
Czaplewski C, Karczynska A, Sieradzan AK, Liwo A (2018) UNRES server for physics-based coarse-grained simulations and predictions of protein structure, dynamics, and thermodynaics. Nucleic Acids Res 46:W304–W309
pubmed: 29718313
pmcid: 6031057
Krupa P, Karczynska AS, Mozolewska MA, Liwo A, Czaplewski C (2020) UNRES-dock protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations. Bioinformatics 2020:1–3. https://doi.org/10.1093/bioinformatics/btaa897
Krokhotin A, Liwo A, Maisuradze GG, Niemi AJ, Scheraga HA (2014) Kinks, loops, and protein folding, with protein a as an example. J Chem Phys 140:025101
pubmed: 24437917
pmcid: 3899063
Masters CL, Simms G, Weinman NA, Multhaup G, McDonald B, Beyreuther K (1985) Amyloid plaque core protein in Alzheimer disease and down syndrome. Proc Natl Acad Sci U S A 82:4245–4249
pubmed: 3159021
pmcid: 397973
Kampinga HH, Craig EA (2010) The HSP70 chaperone machinery: J proteins as drivers of functional specificity. Nat Rev Mol Cell Biol 11:579–592
Kityk R, Kopp J, Sinning I, Mayer MP (2012) Structure and dynamics of the ATP-bound open conformation of Hsp70 chaperones. Mol Cell 48:863–874
pubmed: 23123194
Lill R, Muhlenhoff U (2008) Maturation of iron-sulfur proteins in eukaryotes: mechanisms, connected processes, and diseases. Annu Rev Biochem 77:669–700
Zhang Y (2008) ITASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40
pubmed: 18215316
pmcid: 2245901
Venselaar H, Joosten R, Vroling B, Baakaman C, Hekkelman M, Krieger E, Vriend G (2010) Homology modelling and spectroscopy, a never-ending love story. Eur Biophys J 39:551–563
pubmed: 19718498
Pierce B, Hourai Y, Weng Z (2011) Accelerating protein docking in ZDOCK using an advanced 3D convolution library. PLoS One 6:e24657
pubmed: 21949741
pmcid: 3176283