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Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

Zhou R, Maisuradze GG, Suñol D, Todorovski T, Macias MJ, Xiao Y, Scheraga HA, Czaplewski C, Liwo A
Proc Natl Acad Sci U S A 111 18243-8 (2014)
Related entries: 2mw9, 2mwb, 2mwd, 2mwe, 2mwf

Cited: 18 times
EuropePMC logo PMID: 25489078

Abstract

To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.

Articles - 2mwa mentioned but not cited (1)

  1. Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements. Zhou R, Maisuradze GG, Suñol D, Todorovski T, Macias MJ, Xiao Y, Scheraga HA, Czaplewski C, Liwo A. Proc Natl Acad Sci U S A 111 18243-18248 (2014)


Articles citing this publication (17)

  1. 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. Liwo A, Sieradzan AK, Lipska AG, Czaplewski C, Joung I, Żmudzińska W, Hałabis A, Ołdziej S. J Chem Phys 150 155104 (2019)
  2. Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems. Liwo A, Czaplewski C, Sieradzan AK, Lipska AG, Samsonov SA, Murarka RK. Biomolecules 11 1347 (2021)
  3. Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning. Matsunaga Y, Sugita Y. Elife 7 e32668 (2018)
  4. Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach. He Y, Liwo A, Scheraga HA. J Chem Phys 143 243111 (2015)
  5. Preventing fibril formation of a protein by selective mutation. Maisuradze GG, Medina J, Kachlishvili K, Krupa P, Mozolewska MA, Martin-Malpartida P, Maisuradze L, Macias MJ, Scheraga HA. Proc Natl Acad Sci U S A 112 13549-13554 (2015)
  6. Sequence-Based Prediction of Metamorphic Behavior in Proteins. Chen N, Das M, LiWang A, Wang LP. Biophys J 119 1380-1390 (2020)
  7. High-Resolution Mapping of the Folding Transition State of a WW Domain. Dave K, Jäger M, Nguyen H, Kelly JW, Gruebele M. J Mol Biol 428 1617-1636 (2016)
  8. Toward a quantitative description of microscopic pathway heterogeneity in protein folding. Gopi S, Singh A, Suresh S, Paul S, Ranu S, Naganathan AN. Phys Chem Chem Phys 19 20891-20903 (2017)
  9. Missense Mutations Modify the Conformational Ensemble of the α-Synuclein Monomer Which Exhibits a Two-Phase Characteristic. Guzzo A, Delarue P, Rojas A, Nicolaï A, Maisuradze GG, Senet P. Front Mol Biosci 8 786123 (2021)
  10. Role of the sulfur to α-carbon thioether bridges in thurincin H. Mozolewska MA, Sieradzan AK, Niadzvedstki A, Czaplewski C, Liwo A, Krupa P. J Biomol Struct Dyn 35 2868-2879 (2017)
  11. Wild-Type α-Synuclein and Variants Occur in Different Disordered Dimers and Pre-Fibrillar Conformations in Early Stage of Aggregation. Guzzo A, Delarue P, Rojas A, Nicolaï A, Maisuradze GG, Senet P. Front Mol Biosci 9 910104 (2022)
  12. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction. Lipska AG, Seidman SR, Sieradzan AK, Giełdoń A, Liwo A, Scheraga HA. J Chem Phys 144 184110 (2016)
  13. Mechanistic Kinetic Model Reveals How Amyloidogenic Hydrophobic Patches Facilitate the Amyloid-β Fibril Elongation. Xie H, Rojas A, Maisuradze GG, Khelashvili G. ACS Chem Neurosci 13 987-1001 (2022)
  14. New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain. Kachlishvili K, Korneev A, Maisuradze L, Liu J, Scheraga HA, Molochkov A, Senet P, Niemi AJ, Maisuradze GG. J Phys Chem B 124 3855-3872 (2020)
  15. Reoptimized UNRES Potential for Protein Model Quality Assessment. Faraggi E, Krupa P, Mozolewska MA, Liwo A, Kloczkowski A. Genes (Basel) 9 E601 (2018)
  16. Early Stages of RNA-Mediated Conversion of Human Prions. Lubecka EA, Hansmann UHE. J Phys Chem B 126 6221-6230 (2022)
  17. Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin. Danielsson A, Samsonov SA, Liwo A, Sieradzan AK. J Chem Theory Comput 19 6023-6036 (2023)


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