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Arsiccio A, Ganguly P, Shea JE. A Transfer Free Energy Based Implicit Solvent Model for Protein Simulations in Solvent Mixtures: Urea-Induced Denaturation as a Case Study. J Phys Chem B 2022; 126:4472-4482. [PMID: 35679169 DOI: 10.1021/acs.jpcb.2c00889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We developed a method for implicit solvent molecular dynamics simulations of proteins in solvent mixtures (model with implicit solvation thermodynamics, MIST). The MIST method introduces experimental group transfer free energies to the generalized Born formulation for generating molecular trajectories without the need for developing rigorous explicit-solvent force fields for multicomponent solutions. As a test case, we studied the urea-induced denaturation of the Trp-cage miniprotein in water. We demonstrate that our method allows efficient exploration of the conformational space of the protein in only a few hundreds of nanoseconds of all-atom unbiased simulations. Furthermore, selective implementation of the transfer free energies of specific peptide groups, backbone, and side chains enables us to decouple their specific energetic contributions to the conformational changes of the protein. The approach herein developed can readily be extended to the investigation of complex matrices as well as to the characterization of protein aggregation. The MIST method is implemented in Plumed (ver. 2.8) as a separate module called SASA.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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Hormann J, van der Meer M, Sarkar B, Kulak N. From Cyclen to 12-Crown-4 Copper(II) Complexes: Exchange of Donor Atoms Improves DNA Cleavage Activity. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500596] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hu Y, Meng J, Shi C, Hervin K, Fratamico PM, Shi X. Characterization and comparative analysis of a second thermonuclease from Staphylococcus aureus. Microbiol Res 2013; 168:174-82. [DOI: 10.1016/j.micres.2012.09.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/12/2012] [Accepted: 09/14/2012] [Indexed: 12/12/2022]
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4
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Wang M, Feng Y, Yao H, Wang J. Importance of the C-terminal loop L137-S141 for the folding and folding stability of staphylococcal nuclease. Biochemistry 2010; 49:4318-26. [PMID: 20415411 DOI: 10.1021/bi100118k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of the C-terminal loop L137-S141 in the folding and folding stability of staphylococcal nuclease (SNase) was investigated by deletion mutation. The C-terminal truncated SNase fragments, SNase137, SNase139, SNase140, and SNase141 containing residues 1-137, 1-139, 1-140, and 1-141, respectively, were adopted in this study. Folding states of these four SNase fragments were analyzed by circular dichroism and fluorescence measurements. The solution structure of SNase140 was determined and compared to those of SNase141 and native SNase using the heteronuclear NMR method. The results showed that folding of the four SNase fragments is correlated with the folding of helix alpha3. With the chain length extending from L137 and I139 to S141, folding of the fragments progressively approached to the tertiary folding of native SNase, and the folding stability was enhanced. These observations revealed that the C-terminal loop L137-S141 has profound effect not only on the folding of helix alpha3 but also on the stabilizing folding of both the alpha- and beta-subdomains of SNase. Analysis indicates that stabilizing folding of the SNase and SNase fragments depends to a large extent on the hydrophobic packing interactions in both the C-terminal local structural region surrounding W140 including the loop L137-S141 and the N-terminal local structural region of the "beta-barrel" hydrophobic core.
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Affiliation(s)
- Min Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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Wei H, Fan Y, Gao YQ. Effects of Urea, Tetramethyl Urea, and Trimethylamine N-Oxide on Aqueous Solution Structure and Solvation of Protein Backbones: A Molecular Dynamics Simulation Study. J Phys Chem B 2009; 114:557-68. [DOI: 10.1021/jp9084926] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Haiyan Wei
- Department of Chemistry, P.O. Box 3012, Texas A&M University, College Station, Texas 77842
| | - Yubo Fan
- Department of Chemistry, P.O. Box 3012, Texas A&M University, College Station, Texas 77842
| | - Yi Qin Gao
- Department of Chemistry, P.O. Box 3012, Texas A&M University, College Station, Texas 77842
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Geng Y, Feng Y, Xie T, Shan L, Wang J. The Native-like Interactions between SNase121 and SNase(111−143) Fragments Induce the Recovery of Their Native-like Structures and the Ability to Degrade DNA. Biochemistry 2009; 48:8692-703. [DOI: 10.1021/bi901099s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yong Geng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Yingang Feng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Tao Xie
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Lu Shan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Jinfeng Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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Fang X, Cui Q, Tong Y, Feng Y, Shan L, Huang L, Wang J. A stabilizing alpha/beta-hydrophobic core greatly contributes to hyperthermostability of archaeal [P62A]Ssh10b. Biochemistry 2008; 47:11212-21. [PMID: 18821773 DOI: 10.1021/bi8007593] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hyperthermophilic Ssh10b from Sulfolobus shibatae is a member of the Sac10b family, which has been postulated to play a role in chromosomal organization in Archaea. Ssh10b is capable of significantly constraining negative DNA supercoils at elevated temperatures. In this study, the solution structure of the dimeric P62A mutant Ssh10b ([P62A]Ssh10b) was determined by multidimensional NMR spectroscopy. The backbone 15N dynamics, H/D exchange with and without the denaturant GdmSCN, and chemical and thermal denaturation experiments were performed to investigate the molecular basis of high thermostability of [P62A]Ssh10b. Data analysis has revealed an alpha/beta-hydrophobic core consisting of two alpha-helices and one beta-sheet which are stabilized by cooperative hydrophobic and hydrogen-bonding interactions. This stabilizing alpha/beta-hydrophobic core of [P62A]Ssh10b exhibiting highly restricted internal motions is composed of residues having highly protected amide protons which exchange with solvent mostly by means of a global unfolding process. The K40N mutation greatly destabilizes the mutant [P62A]Ssh10b because this mutation disturbs the packing of alpha-helix against the beta-sheet reducing the stability of the alpha/beta-hydrophobic core in the mutant protein. In comparison with homologous mesophilic and thermophilic proteins, it can be presumed that the stabilizing alpha/beta-hydrophobic core in the [P62A]Ssh10b structure greatly contributes to the high thermostability of the protein.
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Affiliation(s)
- Xianyang Fang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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Libich DS, Harauz G. Solution NMR and CD spectroscopy of an intrinsically disordered, peripheral membrane protein: evaluation of aqueous and membrane-mimetic solvent conditions for studying the conformational adaptability of the 18.5 kDa isoform of myelin basic protein (MBP). EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:1015-29. [PMID: 18449534 DOI: 10.1007/s00249-008-0334-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Revised: 04/09/2008] [Accepted: 04/11/2008] [Indexed: 02/05/2023]
Abstract
The stability and secondary structure propensity of recombinant murine 18.5 kDa myelin basic protein (rmMBP, 176 residues) was assessed using circular dichroic and nuclear magnetic resonance spectroscopy (1H-15N HSQC experiments) to determine the optimal sample conditions for further NMR studies (i.e., resonance assignments and protein-protein interactions). Six solvent conditions were selected based on their ability to stabilise the protein, and their tractability to currently standard solution NMR methodology. Selected solvent conditions were further characterised as functions of concentration, temperature, and pH. The results of these trials indicated that 30% TFE-d2 in H2O (v/v), pH 6.5 at 300 K, and 100 mM KCl, pH 6.5 at 277 K were the best conditions to use for future solution NMR studies of MBP. Micelles of DPC were found to be inappropriate for backbone resonance assignments of rmMBP in this instance.
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Affiliation(s)
- David S Libich
- Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, ON, Canada
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