Protein structure and dynamics in nonaqueous solvents: Insights from molecular dynamics simulation studies

Soares, Cláudio M.; Teixeira, Vitor H.; Baptista, António M.

doi:10.1016/s0006-3495(03)74972-8

Cited by 149Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsLipid Membrane Structure and Behavior

Protein structure and dynamics in nonaqueous solvents: Insights from molecular dynamics simulation studies

Open access

Soares, Cláudio M., Teixeira, Vitor H., Baptista, António M.·2003·Biophysical Journal

DOI 10.1016/s0006-3495(03)74972-8PMC PMC1302733

Open this paper in CoChat — free account Open PDF

Abstract

Protein structure and dynamics in nonaqueous solvents are here investigated using molecular dynamics simulation studies, by considering two model proteins (ubiquitin and cutinase) in hexane, under varying hydration conditions. Ionization of the protein groups is treated assuming "pH memory," i.e., using the ionization states characteristic of aqueous solution. Neutralization of charged groups by counterions is done by considering a counterion for each charged group that cannot be made neutral by establishing a salt bridge with another charged group; this treatment is more physically reasonable for the nonaqueous situation, contrasting with the usual procedures. Our studies show that hydration has a profound effect on protein stability and flexibility in nonaqueous solvents. The structure becomes more nativelike with increasing values of hydration, up to a certain point, when further increases render it unstable and unfolding starts to occur. There is an optimal amount of water, approximately 10% (w/w), where the protein structure and flexibility are closer to the ones found in aqueous solution. This behavior can explain the experimentally known bell-shaped dependence of enzyme catalysis on hydration, and the molecular reasons for it are examined here. Water and counterions play a fundamental and dynamic role on protein stabilization, but they also seem to be important for protein unfolding at high percentages of bound water.

Integrity signals

Registry

Crossref · 10.1016/s0006-3495(03)74972-8

Cites

76 of 76 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

The structures of proteins change depending on solvent polarity, and would be expected to change within polyester droplets compared to polar solvents.
“As another example, the structures of proteins change depending on solvent polarity, and would be expected to change within polyester droplets compared to polar solvents [67,68].”
From Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry (2020) · cites this paper as [67]

Molecular dynamics with coupling to an external bath
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984) · The Journal of Chemical Physics · doi:10.1063/1.448118 · Cited by 30,626 · see citing works
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
Ryckaert, J., Ciccotti, G., & Berendsen, H. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90098-5 · Cited by 19,525 · see citing works
Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320 · see citing works
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Kraulis, P. J. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891004399 · Cited by 14,011 · see citing works
[26] Raster3D: Photorealistic molecular graphics
Merritt, E. A., & Bacon, D. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)77028-9 · Cited by 3,749 · see citing works
Improving enzymes by using them in organic solvents
Klibanov, A. M. (2001) · Nature · doi:10.1038/35051719 · Cited by 2,152 · see citing works
Structure of ubiquitin refined at 1.8 Å resolution
Vijay‐Kumar, S., Bugg, C. E., & Cook, W. J. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90679-6 · Cited by 1,753 · see citing works
Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry
van Gunsteren, W. F., & Berendsen, H. J. C. (1990) · Angewandte Chemie International Edition in English · doi:10.1002/anie.199009921 · Cited by 1,560 · see citing works
The GROMOS Biomolecular Simulation Program Package
Scott, W. R. P., Hünenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Krüger, P., & A, W. F. V. G. (1999) · The Journal of Physical Chemistry A · doi:10.1021/jp984217f · Cited by 1,489 · see citing works
A generalized reaction field method for molecular dynamics simulations
Tironi, I. G., Sperb, R. P., Smith, P. E., & A, W. F. V. G. (1995) · The Journal of Chemical Physics · doi:10.1063/1.469273 · Cited by 1,443 · see citing works
Automated docking of substrates to proteins by simulated annealing
Goodsell, D. S., & Olson, A. J. (1990) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340080302 · Cited by 1,288 · see citing works
Enzyme-catalyzed processes in organic solvents.
Zaks, A., & Klibanov, A. M. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.10.3192 · Cited by 1,239 · see citing works
pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model
Bashford, D., & Karplus, M. (1990) · Biochemistry · doi:10.1021/bi00496a010 · Cited by 1,089 · see citing works
Enzymatic Catalysis in Organic Media at 100°C
Zaks, A., & Klibanov, A. M. (1984) · Science · doi:10.1126/science.6729453 · Cited by 1,063 · see citing works
Enzymatic catalysis in nonaqueous solvents.
Zaks, A., & Klibanov, A. M. (1988) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)69054-4 · Cited by 995 · see citing works
The effect of water on enzyme action in organic media.
Zaks, A., & Klibanov, A. M. (1988) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)68435-2 · Cited by 926 · see citing works
A consistent empirical potential for water–protein interactions
Hermans, J., Berendsen, H. J. C., A, W. F. V. G., & Postma, J. P. M. (1984) · Biopolymers · doi:10.1002/bip.360230807 · Cited by 774 · see citing works
Monte Carlo studies of the dielectric properties of water-like models
Barker, J. A., & Watts, R. O. (1973) · Molecular Physics · doi:10.1080/00268977300102101 · Cited by 716 · see citing works
A visual protein crystallographic software system for X11/Xview
McRee, D. E. (1992) · Journal of Molecular Graphics · doi:10.1016/0263-7855(92)80022-6 · Cited by 550 · see citing works
Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin
Bashford, D., & Gerwert, K. B. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)91009-e · Cited by 549 · see citing works
On the calculation of pKas in proteins
Yang, A., Gunner, M. R., Sampogna, R. V., Sharp, K. A., & Honig, B. H. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340150304 · Cited by 508 · see citing works
How do serine proteases really work?
Warshel, A., Náray‐Szabó, G., Sussman, F., & Hwang, J.-K. (1989) · Biochemistry · doi:10.1021/bi00435a001 · Cited by 462 · see citing works
Water and globular proteins
Rupley, J. A., Gratton, E., & Careri, G. (1983) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(83)90063-4 · Cited by 445 · see citing works
On Protein Denaturation in Aqueous−Organic Mixtures but Not in Pure Organic Solvents
Griebenow, K. H., & Klibanov, A. M. (1996) · Journal of the American Chemical Society · doi:10.1021/ja961869d · Cited by 402 · see citing works
Calculations of enzymic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes
Warshel, A. (1981) · Biochemistry · doi:10.1021/bi00514a028 · Cited by 319 · see citing works
Constant-pH molecular dynamics using stochastic titration
Baptista, A. M., Teixeira, V., & Soares, C. M. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1497164 · Cited by 311 · see citing works
Self-citation
Electrostatic effects in proteins: comparison of dielectric and charge models
Mehler, E. L., & Solmajer, T. (1991) · Protein Engineering Design and Selection · doi:10.1093/protein/4.8.903 · Cited by 280 · see citing works
Enzymatic catalysis and dynamics in low-water environments.
Affleck, R., Xu, Z. F., Suzawa, V. M., et al. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.3.1100 · Cited by 254 · see citing works
Atomic resolution (1.0 Å) crystal structure of Fusarium solani cutinase: stereochemical analysis
Longhi, S., Czjzek, M., Lamzin, V. S., Nicolas, A., & Cambillau, C. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1000 · Cited by 234 · see citing works
Enzyme crystal structure in a neat organic solvent.
Fitzpatrick, P., Steinmetz, A. C. U., Ringe, D., et al. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.18.8653 · Cited by 230 · see citing works
Biocatalyst behaviour in low-water systems
Bell, G., Halling, P. J., Moore, B. D., et al. (1995) · Trends in biotechnology · doi:10.1016/s0167-7799(00)89004-6 · Cited by 208 · see citing works
Correlation of IR spectroscopic, heat capacity, diamagnetic susceptibility and enzymatic measurements on lysozyme powder
Careri, G., Gratton, E., Yang, P.-H., et al. (1980) · Nature · doi:10.1038/284572a0 · Cited by 198 · see citing works
Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K
Smith, P. E., & van Gunsteren, W. F. (1994) · The Journal of Chemical Physics · doi:10.1063/1.466407 · Cited by 193 · see citing works
An Experimental Approach to Mapping the Binding Surfaces of Crystalline Proteins
Allen, K. N., Bellamacina, C. R., Ding, X., Jeffery, C. J., Mattos, C., Petsko, G. A., & Ringe, D. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp952516o · Cited by 186 · see citing works
Cutinase, a lipolytic enzyme with a preformed oxyanion hole
Martinez, C., Nicolas, A., TILBEURGH, H. V., et al. (1994) · Biochemistry · doi:10.1021/bi00167a011 · Cited by 165 · see citing works
Flexibility of Enzymes Suspended in Organic Solvents Probed by Time-Resolved Fluorescence Anisotropy. Evidence That Enzyme Activity and Enantioselectivity Are Directly Related to Enzyme Flexibility
Broos, J., Visser, A. J. W. G., Engbersen, J. F. J., et al. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00156a001 · Cited by 163 · see citing works
Synthesis of Expanded Graphdiyne Substructures
Wan, W., Brand, S. C., Pak, J. J., et al. (2000) · Chemistry - A European Journal · doi:10.1002/1521-3765(20000602)6:11 · Cited by 144 · see citing works
X-ray Crystal Structure of .gamma.-Chymotrypsin in Hexane
Yennawar, N. H., Yennawar, H. P., & Farber, G. K. (1994) · Biochemistry · doi:10.1021/bi00189a038 · Cited by 139 · see citing works
Some Theoretical and Computational Aspects of the Inclusion of Proton Isomerism in the Protonation Equilibrium of Proteins
Baptista, A. M., & Soares, C. M. (2000) · The Journal of Physical Chemistry B · doi:10.1021/jp002763e · Cited by 135 · see citing works
Self-citation
Scientific Computing in Object-Oriented Parallel Environments
Ishikawa, Y., Tholburn, M., Reynders, J. V. W., et al. (1997) · Lecture notes in computer science · doi:10.1007/3-540-63827-x · Cited by 130 · see citing works
Importance of Explicit Salt Ions for Protein Stability in Molecular Dynamics Simulation
Ibragimova, G. T., & Wade, R. C. (1998) · Biophysical Journal · doi:10.1016/s0006-3495(98)77997-4 · Cited by 123 · see citing works
High-affinity binding of water by proteins is similar in air and in organic solvents
Halling, P. J. (1990) · Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology · doi:10.1016/0167-4838(90)90080-y · Cited by 117 · see citing works
Simulation of Electron-Proton Coupling with a Monte Carlo Method: Application to Cytochrome c3 Using Continuum Electrostatics
Baptista, A. M., Martel, P. J., & Soares, C. M. (1999) · Biophysical Journal · doi:10.1016/s0006-3495(99)77452-7 · Cited by 108 · see citing works
Self-citation
A Molecular Dynamics and Quantum Mechanics Analysis of the Effect of DMSO on Enzyme Structure and Dynamics: Subtilisin
Zheng, Y., & Ornstein, R. L. (1996) · Journal of the American Chemical Society · doi:10.1021/ja9539195 · Cited by 107 · see citing works
Prediction of loop geometries using a generalized born model of solvation effects
Rapp, C. S., & Friesner, R. A. (1999) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19990501)35:2 · Cited by 103 · see citing works
Biocatalysis in low-water media: understanding effects of reaction conditions
Halling, P. J. (2000) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(99)00055-1 · Cited by 102 · see citing works
Protein dynamics and solvation in aqueous and nonaqueous environments
Hartsough, D. S., & Merz, K. M. (1993) · Journal of the American Chemical Society · doi:10.1021/ja00068a009 · Cited by 100 · see citing works
Molecular dynamics simulations of an enzyme surrounded by vacuum, water, or a hydrophobic solvent
Norin, M., Hæffner, F., Hult, K., et al. (1994) · Biophysical Journal · doi:10.1016/s0006-3495(94)80515-6 · Cited by 96 · see citing works
Thermodynamic and Related Studies of Water Interacting with Proteins
Rupley, J. A., Pei-yong, Y. A. N. G., & Tollin, G. (1980) · ACS symposium series · doi:10.1021/bk-1980-0127.ch006 · Cited by 92 · see citing works
Automated docking in crystallography: Analysis of the substrates of aconitase
Goodsell, D. S., Lauble, H., Stout, C. D., et al. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340170104 · Cited by 91 · see citing works
pH Control of the Catalytic Activity of Cross-Linked Enzyme Crystals in Organic Solvents
Xu, K., & Klibanov, A. M. (1996) · Journal of the American Chemical Society · doi:10.1021/ja961596m · Cited by 88 · see citing works
X-Ray Crystal Structure of Cross-Linked Subtilisin Carlsberg in Water vs Acetonitrile
Fitzpatrick, P., Ringe, D., & Klibanov, A. M. (1994) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.1994.1098 · Cited by 87 · see citing works
Molecular mechanics modeling of organic backbone of metal-free and coordinated ligands
Bol, J. E., Buning, C., Comba, P., Reedijk, J., & Str�hle, M. (1998) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(19980415)19:5 · Cited by 80 · see citing works
The crystal structure of subtilisin Carlsberg in anhydrous dioxane and its comparison with those in water and acetonitrile
Schmitke, J. L., Stern, L. J., & Klibanov, A. M. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.9.4250 · Cited by 74 · see citing works
A Structural Explanation for Enzyme Memory in Nonaqueous Solvents
Yennawar, H. P., Yennawar, N. H., & Farber, G. K. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00107a001 · Cited by 69 · see citing works
Activity and mobility of subtilisin in low water organic media: hydration is more important than solvent dielectric
Partridge, J., Dennison, P. R., Moore, B. D., et al. (1998) · Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology · doi:10.1016/s0167-4838(98)00086-7 · Cited by 68 · see citing works
Protein flexibility in aqueous and nonaqueous solutions
Hartsough, D. S., & Merz, K. M. (1992) · Journal of the American Chemical Society · doi:10.1021/ja00052a004 · Cited by 66 · see citing works
Dynamics of proteins in different solvent systems: analysis of essential motion in lipases
Peters, G. H. J., van Aalten, D. M. F., Edholm, O., et al. (1996) · Biophysical Journal · doi:10.1016/s0006-3495(96)79428-6 · Cited by 66 · see citing works
Comparison of different schemes to treat long‐range electrostatic interactions in molecular dynamics simulations of a protein crystal
Walser, R., Hünenberger, P. H., & van Gunsteren, W. F. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.1062 · Cited by 56 · see citing works
Comparison of x-ray crystal structures of an acyl-enzyme intermediate of subtilisin Carlsberg formed in anhydrous acetonitrile and in water
Schmitke, J. L., Stern, L. J., & Klibanov, A. M. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.22.12918 · Cited by 52 · see citing works
Rationalization of the Enantioselectivity of Subtilisin in DMF
Colombo, G., Toba, S., & Merz, K. M. (1999) · Journal of the American Chemical Society · doi:10.1021/ja9839062 · Cited by 51 · see citing works
Nativelike Enzyme Properties Are Important for Optimum Activity in Neat Organic Solvents
Griebenow, K. H., Vidal, M., Báez, C., et al. (2001) · Journal of the American Chemical Society · doi:10.1021/ja015889d · Cited by 50 · see citing works
Control of Enzyme Activity in Organic Media by Solid-State Acid−Base Buffers
Zacharis, E. A., Moore, B. D., & Halling, P. J. (1997) · Journal of the American Chemical Society · doi:10.1021/ja972635c · Cited by 49 · see citing works
Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods
Huang, E. S., Koehl, P., Levitt, M., Pappu, R. V., & Ponder, J. W. (1998) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19981101)33:2 · Cited by 49 · see citing works
Electrostatic screening in molecular dynamics simulations
Solmajer, T., & Mehler, E. L. (1991) · Protein Engineering Design and Selection · doi:10.1093/protein/4.8.911 · Cited by 48 · see citing works
Measuring enzyme hydration in nonpolar organic solvents using NMR
Parker, M. C., Moore, B. D., & Blacker, A. J. (1995) · Biotechnology and Bioengineering · doi:10.1002/bit.260460509 · Cited by 46 · see citing works
Cutinase Activity and Enantioselectivity in Supercritical Fluids
Fontes, N., Almeida, M. C., Peres, C., et al. (1998) · Industrial & Engineering Chemistry Research · doi:10.1021/ie970933c · Cited by 37 · see citing works
Solvation and Dynamics of Chymotrypsin in Hexane
Toba, S., Hartsough, D. S., & Merz, K. M. (1996) · Journal of the American Chemical Society · doi:10.1021/ja960153f · Cited by 36 · see citing works
Effect of pressure on the catalytic activity of subtilisin Carlsberg suspended in compressed gases
Fontes, N., Nogueiro, E., Elvas, A. M., et al. (1998) · Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology · doi:10.1016/s0167-4838(97)00200-8 · Cited by 36 · see citing works
Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane
Gao, X., Maldonado, E., Pérez‐Montfort, R., et al. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.18.10062 · Cited by 36 · see citing works
Fluid shear stress induction of the transcriptional activator c-fos in human and bovine endothelial cells, HeLa, and Chinese hamster ovary cells
Ranjan, V., Waterbury, R. G., Xiao, Z., & Diamond, S. L. (2000) · Biotechnology and Bioengineering · doi:10.1002/(sici)1097-0290(19960220)49:4 · Cited by 35 · see citing works
Consequences of Breaking the Asp-His Hydrogen Bond of the Catalytic Triad: Effects on the Structure and Dynamics of the Serine Esterase Cutinase
Lau, E. Y., & Bruice, T. C. (1999) · Biophysical Journal · doi:10.1016/s0006-3495(99)76874-8 · Cited by 25 · see citing works
X-ray studies on two forms of bovine β-trypsin crystals in neat cyclohexane
Zhu, G., Huang, Q., Wang, Z., et al. (1998) · Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology · doi:10.1016/s0167-4838(98)00226-x · Cited by 19 · see citing works
Measuring enzyme motility in organic media using novel H-D exchange methodology
Hutcheon, G. A., Parker, M. C., & Moore, B. D. (2000) · Biotechnology and Bioengineering · doi:10.1002/1097-0290(20001105)70:3 · Cited by 17 · see citing works
Control of Ionization State and Activity of Enzymes in Organic Mediaa
Halling, P. J., Blackwood, A. D., & Moore, B. D. (1996) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.1996.tb33209.x · Cited by 12 · see citing works
Analysis of secretory dynamics and development of media for the controlled secretion of insulin-related peptides from βTC-3 insulinoma cells
Grampp, G. E., Lodish, H. F., & Stephanopoulos, G. N. (1997) · Biotechnology and Bioengineering · doi:10.1002/(sici)1097-0290(19970205)53:3 · Cited by 1 · see citing works

Flagged first, then by citations

Sorted by citations

Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry
Chandru, K., Mamajanov, I., Cleaves, H. J., & Jia, T. Z. (2020) · Life · doi:10.3390/life10010006 · Cited by 47 · see citing works

Imaging of Dihexadecylphosphate Vesicles by AFM and Counterion Effect on Their Size and Stability
Kardassi, D., Tsiourvas, D., & Paleos, C. M. (1997) · Journal of Colloid and Interface Science · doi:10.1006/jcis.1996.4560 · Cited by 12 · see citing works
An electron spin resonance investigation of the 4,5-methylenephenanthrene dianion radical
Casson, D., & Tabner, B. J. (1971) · Journal of the Chemical Society B Physical Organic · doi:10.1039/j29710000479 · Cited by 4 · see citing works
Stabilization of β-octamolybdate with large counterions
Kama, A. B., Dessapt, R., Serier‐Brault, H., et al. (2017) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2017.03.111 · Cited by 6 · see citing works
Counterion correlations and attractions in dense polyelectrolyte solutions
Liverpool, T. B., & Müller-Nedebock, K. K. (2006) · Journal of Physics Condensed Matter · doi:10.1088/0953-8984/18/10/l01 · Cited by 5 · see citing works
THE EFFECT OF COUNTERIONS ON THE J-AGGREGATION OF AN ANIONIC CYANINE DYE
Zhou, J. (1989) · Ganguang kexue yu guanghuaxue

Authors: Soares, C. M., Teixeira, V. H., & Baptista, A. M.
Affiliations: Universidade Nova de Lisboa (PT)
Corresponding author: Soares, Cláudio M.
ORCID: Soares, Cláudio M.
Baptista, António M.
Venue: Biophysical Journal
Publisher: Elsevier BV
Published: 2003-03
Volume: 84
Issue: 3
Pages: 1628-1641
ISSN: 0006-3495 (ISSN-L)
DOI: 10.1016/s0006-3495(03)74972-8
PMC: PMC1302733
OpenAlex: W2034809628
Cited by: 149
References: 76
Citations by year: 2026: 5 · 2025: 11 · 2024: 5 · 2023: 3 · 2022: 1 · 2021: 8 · 2020: 9 · 2019: 5 · 2018: 3 · 2017: 8 · 2016: 8 · 2015: 8 · 2014: 5 · 2013: 8 · 2012: 10
FWCI: 2.06
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 3790 d)
Locations: Biophysical Journal (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
Keywords: protein hydration, ubiquitin, cutinase, n-hexane, protein unfolding, protein flexibility, ionization state, enzyme catalysis, bound water, protein stability
MeSH terms: Carboxylic Ester Hydrolases, Catalysis, Computer Simulation, Enzyme Activation, Enzyme Stability, Enzymes, Hexanes, Hydrogen-Ion Concentration, Models, Molecular, Motion, Protein Binding, Protein Conformation, Proteins, Sensitivity and Specificity, Solvents, Water, Protein Folding, Ubiquitin

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Protein structure and dynamics in nonaqueous solvents: Insights from molecular dynamics simulation studies

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Cites

Cited by

Related

Record

About these checks