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Huo X, Ji L, Zhang Y, Lv P, Cao X, Wang Q, Yan Z, Dong S, Du D, Zhang F, Wei G, Liu Y, Wen B. The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation. Mol Cell 2019; 77:368-383.e7. [PMID: 31677973 DOI: 10.1016/j.molcel.2019.10.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/24/2019] [Accepted: 09/30/2019] [Indexed: 12/16/2022]
Abstract
Interphase chromatin is hierarchically organized into higher-order architectures that are essential for gene functions, yet the biomolecules that regulate these 3D architectures remain poorly understood. Here, we show that scaffold attachment factor B (SAFB), a nuclear matrix (NM)-associated protein with RNA-binding functions, modulates chromatin condensation and stabilizes heterochromatin foci in mouse cells. SAFB interacts via its R/G-rich region with heterochromatin-associated repeat transcripts such as major satellite RNAs, which promote the phase separation driven by SAFB. Depletion of SAFB leads to changes in 3D genome organization, including an increase in interchromosomal interactions adjacent to pericentromeric heterochromatin and a decrease in genomic compartmentalization, which could result from the decondensation of pericentromeric heterochromatin. Collectively, we reveal the integrated roles of NM-associated proteins and repeat RNAs in the 3D organization of heterochromatin, which may shed light on the molecular mechanisms of nuclear architecture organization.
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Affiliation(s)
- Xiangru Huo
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Luzhang Ji
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yuwen Zhang
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Pin Lv
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xuan Cao
- CAS Key Laboratory of Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qianfeng Wang
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zixiang Yan
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Shuangshuang Dong
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| | - Duo Du
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yun Liu
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Bo Wen
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China.
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Djikaev Y, Ruckenstein E. Recent developments in the theoretical, simulational, and experimental studies of the role of water hydrogen bonding in hydrophobic phenomena. Adv Colloid Interface Sci 2016; 235:23-45. [PMID: 27312562 DOI: 10.1016/j.cis.2016.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/27/2016] [Accepted: 05/10/2016] [Indexed: 10/21/2022]
Abstract
Hydrophobic effects (hydrophobic hydration and hydrophobic interaction) constitute an important element of a wide variety of phenomena relevant to biological, physical, chemical, environmental, engineering, and pharmaceutical sciences, such as the immiscibility of oil and water, self-assembly of amphiphiles leading to micelle and membrane formation, folding and stability and unfolding of the native structure of a biologically active protein, gating of ion channels, wetting, froth floatation, and adhesion. On the other hand, the hydrogen bonding ability of water plays a major (if not crucial) role in hydrophobic phenomena. We present a review of most important and relatively recent experimental, simulational, and theoretical research on hydrophobic phenomena in various systems. With a particular interest we survey investigations clarifying the role of water hydrogen bonding therein, because it has been the main object of our own recent research. We have developed a probabilistic hydrogen bond (PHB) model that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of its distance to a hydrophobe, hydrophobe radius, and temperature. Knowing that function, one can explicitly identify a water hydrogen bond contribution to the external potential whereto a water molecule is subjected near a hydrophobe. Combining the PHB model with the classical density functional theory (DFT), one can examine the contribution of water hydrogen bonding to the temperature and lengthscale effects on the hydration of particles and on their solvent-mediated interactions over the entire low-to-high temperature and small-to-large lengthscale ranges. We applied the combined DFT/PHB model to study a variety of hydrophobic phenomena such as (liquid) water in contact with a hydrophobic plate, solvation of spherical solutes of various radii in associated and non-associated liquids at various temperatures, the solvent-mediated interaction of spherical solutes and its temperature dependence, interaction of C60 fullerenes in water, temperature effect on the evaporation lengthscale of water confined between two hydrophobes, temperature dependence of the effective width of the solute-solvent transition layer and average density therein. These applications demonstrated that the DFT/PHB model can serve as a valuable tool in studying hydrophobic phenomena because it constitutes a balanced combination of simplicity, accuracy, and detail. The predictions of the combined DFT/PHB approach for the solvent density profiles and thermodynamic aspects of hydrophobic phenomena are generally in good agreement with experiments and simulations. For example, it predicts the small-to-large crossover lengthscale of its mechanism to be approximately in the range from 1nm to 4nm, and decreasing with increasing temperature. It also suggests that, in terms of the average fluid density in the solute-solvent transition layer, the transition layer for small hydrophobes (of radii ≲2 nm) becomes enriched with rather than depleted of fluid when both the solvent-solute affinity and hb-energy alteration ratio become large enough. The boundary values of these parameters, needed for the depletion-to-enrichment crossover, are predicted to decrease with increasing temperature.
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Djikaev YS, Ruckenstein E. Temperature dependence of the evaporation lengthscale for water confined between two hydrophobic plates. J Colloid Interface Sci 2015; 449:226-35. [PMID: 25708521 DOI: 10.1016/j.jcis.2015.01.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/20/2015] [Indexed: 11/20/2022]
Abstract
Liquid water in a hydrophobic confinement is the object of high interest in physicochemical sciences. Confined between two macroscopic hydrophobic surfaces, liquid water transforms into vapor if the distance between surfaces is smaller than a critical separation, referred to as the evaporation lengthscale. To investigate the temperature dependence of the evaporation lengthscale of water confined between two hydrophobic parallel plates, we use the combination of the density functional theory (DFT) with the probabilistic hydrogen bond (PHB) model for water-water hydrogen bonding. The PHB model provides an analytic expression for the average number of hydrogen bonds per water molecule as a function of its distance to a hydrophobic surface and its curvature. Knowing this expression, one can implement the effect of hydrogen bonding between water molecules on their interaction with the hydrophobe into DFT, which is then employed to determine the distribution of water molecules between two macroscopic hydrophobic plates at various interplate distances and various temperatures. For water confined between hydrophobic plates, our results suggest the evaporation lengthscale to be of the order of several nanometers and a linearly increasing function of temperature from T=293 K to T=333 K, qualitatively consistent with previous results.
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Affiliation(s)
- Yuri S Djikaev
- Department of Chemical and Biological Engineering, SUNY at Buffalo, Buffalo, NY 14260, United States.
| | - Eli Ruckenstein
- Department of Chemical and Biological Engineering, SUNY at Buffalo, Buffalo, NY 14260, United States.
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Djikaev YS, Ruckenstein E. The solvent-induced interaction of spherical solutes in associated and non-associated liquids. J Chem Phys 2014; 141:034705. [PMID: 25053332 DOI: 10.1063/1.4886808] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We propose an efficient method for studying the solvent-induced interaction of two solvophobic particles immersed in a liquid solvent. The method is based on the combination of the probabilistic hydrogen bond model with the density functional theory. An analytic expression for the number of hydrogen bonds per water molecule near two spherical hydrophobes is derived as a function of the molecule distance to both hydrophobes, distance between hydrophobes, and their radii. Using this expression, one can construct an approximation for the distribution of fluid (liquid water) molecules in the system which provides a reasonably good (much faster and accurate enough) alternative to a standard iteration procedure. Such an approximate density distribution constitutes an efficient foundation for studying the length-scale and temperature dependence of hydrophobic interactions. The model is applied to the interaction of solvophobic solutes in both associated and non-associated liquids. Of these two cases, the model predictions for the solvent-induced potential of mean force between two solutes in associated liquids are closer to the results of molecular dynamics simulation of hydrophobic interactions in the SPC/E model water. Our results suggest that the hydrogen bonding ability of water molecules may play a major role in hydrophobic phenomena.
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Affiliation(s)
- Yuri S Djikaev
- Department of Chemical and Biological Engineering, SUNY at Buffalo, Buffalo, New York 14260, USA
| | - Eli Ruckenstein
- Department of Chemical and Biological Engineering, SUNY at Buffalo, Buffalo, New York 14260, USA
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Tabor RF, Grieser F, Dagastine RR, Chan DYC. The hydrophobic force: measurements and methods. Phys Chem Chem Phys 2014; 16:18065-75. [DOI: 10.1039/c4cp01410c] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The hydrophobic force describes the attraction between water-hating molecules (and surfaces) that draws them together, causing aggregation, phase separation, protein folding and many other inherent physical phenomena.
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Affiliation(s)
- Rico F. Tabor
- School of Chemistry
- Monash University
- Clayton, Australia
| | - Franz Grieser
- Particulate Fluids Processing Centre
- The University of Melbourne
- Parkville 3010, Australia
- School of Chemistry
- The University of Melbourne
| | - Raymond R. Dagastine
- Particulate Fluids Processing Centre
- The University of Melbourne
- Parkville 3010, Australia
- Department of Chemical and Biomolecular Engineering
- The University of Melbourne
| | - Derek Y. C. Chan
- Particulate Fluids Processing Centre
- The University of Melbourne
- Parkville 3010, Australia
- Department of Mathematics and Statistics
- The University of Melbourne
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Calixarene building block bis(2-hydroxyphenyl)methane (2HDPM) and hydrogen-bonded 2HDPM-H2O complex in electronic excited state. J Mol Model 2013; 19:1913-8. [DOI: 10.1007/s00894-012-1710-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/26/2012] [Indexed: 10/27/2022]
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Measurement and analysis of forces in bubble and droplet systems using AFM. J Colloid Interface Sci 2012; 371:1-14. [DOI: 10.1016/j.jcis.2011.12.047] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 12/14/2011] [Accepted: 12/15/2011] [Indexed: 11/17/2022]
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Djikaev YS, Ruckenstein E. Effect of Water–Water Hydrogen Bonding on the Hydrophobic Hydration of Large-Scale Particles and Its Temperature Dependence. J Phys Chem B 2012; 116:2820-30. [DOI: 10.1021/jp2102435] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Y. S. Djikaev
- Department of Chemical & Biological Engineering, SUNY at Buffalo, Buffalo, New York 14260, United States
| | - E. Ruckenstein
- Department of Chemical & Biological Engineering, SUNY at Buffalo, Buffalo, New York 14260, United States
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Djikaev Y, Ruckenstein E. The variation of the number of hydrogen bonds per water molecule in the vicinity of a hydrophobic surface and its effect on hydrophobic interactions. Curr Opin Colloid Interface Sci 2011. [DOI: 10.1016/j.cocis.2010.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ho TA, Argyris D, Papavassiliou DV, Striolo A, Lee LL, Cole DR. Interfacial water on crystalline silica: a comparative molecular dynamics simulation study. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.513008] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Djikaev YS, Ruckenstein E. Dependence of the number of hydrogen bonds per water molecule on its distance to a hydrophobic surface and a thereupon-based model for hydrophobic attraction. J Chem Phys 2010; 133:194105. [DOI: 10.1063/1.3499318] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Temperature effects on the hydrophobic interaction of parallel plates in the framework of the probabilistic approach to hydrogen bonding. J Colloid Interface Sci 2010; 343:510-21. [DOI: 10.1016/j.jcis.2009.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 11/30/2009] [Accepted: 12/02/2009] [Indexed: 11/20/2022]
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A probabilistic approach to the effect of water hydrogen bonds on the kinetics of protein folding and protein denaturation. Adv Colloid Interface Sci 2010; 154:77-90. [PMID: 20163782 DOI: 10.1016/j.cis.2010.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 01/20/2010] [Indexed: 11/23/2022]
Abstract
Previously, we presented a review of our kinetic models for the nucleation mechanism of protein folding and for the protein thermal denaturation in a barrierless way. A protein was treated as a random heteropolymer consisting of hydrophobic, hydrophilic, and neutral beads. As a crucial idea of the model, an overall potential around the cluster of native residues wherein a residue performs a chaotic motion was considered as the combination of the average dihedral, effective pairwise, and confining potentials. The overall potential as a function of the distance from the cluster has a double well shape. This allowed one to develop kinetic models for the nucleation mechanism of protein folding (NMPF) and barrierless protein denaturation (BPD) by using the mean first passage time analysis. In the original models, however, hydrogen bonding effects were taken into account only indirectly which affected the accuracy of the models because hydrogen bonding does play a crucial role in the folding, stability, and denaturation of proteins. To improve the NMPF and BPD models and explicitly take into account the hydrogen bonding "water-water" and "water-protein residue", we have developed a probabilistic hydrogen bond (PHB) model for the effect of hydrogen bond networks of water molecules around two solute particles (immersed in water) on their interaction, and have then combined the PHB model with the NMPF and BPD models. In this paper, that can be regarded as sequel of our previous review, we analyze the modified NMPF and BPD models that explicitly take into account the effect of water-water hydrogen bonding on these processes. As expected, the application of the modified models to the folding/unfolding of two model proteins (one short, consisting of 124 residues and the other large, consisting of 2500 residues) demonstrate that the hydrogen bond networks play a very important role in the protein folding/unfolding phenomena.
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Wei N, Li P, Hao C, Wang R, Xiu Z, Chen J, Song P. Time-dependent density functional theory study of the excited-state dihydrogen bond O–H⋯H–Si. J Photochem Photobiol A Chem 2010. [DOI: 10.1016/j.jphotochem.2009.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Wei NN, Hao C, Xiu Z, Qiu J. Time-dependent density functional theory study on the coexistent intermolecular hydrogen-bonding and dihydrogen-bonding of the phenol-H2O-diethylmethylsilane complex in electronic excited states. Phys Chem Chem Phys 2010; 12:9445-51. [DOI: 10.1039/b927049c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Djikaev YS, Ruckenstein E. Effect of hydrogen bond networks on the nucleation mechanism of protein folding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:061918. [PMID: 20365201 DOI: 10.1103/physreve.80.061918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/23/2009] [Indexed: 05/29/2023]
Abstract
We have recently developed a kinetic model for the nucleation mechanism of protein folding (NMPF) in terms of ternary nucleation by using the first passage time analysis. A protein was considered as a random heteropolymer consisting of hydrophobic, hydrophilic (some of which are negatively or positively ionizable), and neutral beads. The main idea of the NMPF model consisted of averaging the dihedral potential in which a selected residue is involved over all possible configurations of all neighboring residues along the protein chain. The combination of the average dihedral, effective pairwise (due to Lennard-Jones-type and electrostatic interactions), and confining (due to the polymer connectivity constraint) potentials gives rise to an overall potential around the cluster that, as a function of the distance from the cluster center, has a double-well shape. This allows one to evaluate the protein folding time. In the original NMPF model hydrogen bonding was not taken into account explicitly. To improve the NMPF model and make it more realistic, in this paper we modify our (previously developed) probabilistic hydrogen bond model and combine it with the former. Thus, a contribution due to the disruption of hydrogen bond networks around the interacting particles (cluster of native residues and residue in the protein unfolded part) appears in the overall potential field around a cluster. The modified model is applied to the folding of the same model proteins that were examined in the original model: a short protein consisting of 124 residues (roughly mimicking bovine pancreatic ribonuclease) and a long one consisting of 2500 residues (as a representative of large proteins with superlong polypeptide chains), at pH=8.3 , 7.3, and 6.3. The hydrogen bond contribution now plays a dominant role in the total potential field around the cluster (except for very short distances thereto where the repulsive energy tends to infinity). It is by an order of magnitude stronger for hydrophobic residues than for hydrophilic ones. The range of "residue-cluster" distances, at which the hydrogen bond effect exists, is twice as long for hydrophobic residues as for hydrophilic ones.
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Affiliation(s)
- Y S Djikaev
- Department of Chemical and Biological Engineering, SUNY at Buffalo, Buffalo, New York 14260, USA.
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Djikaev YS, Ruckenstein E. The role of hydrogen bond networks in the barrierless thermal denaturation of a native protein. J Chem Phys 2009; 131:045105. [DOI: 10.1063/1.3179688] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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