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Chen X, Leyendecker S, van den Bedem H. Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease. J Chem Inf Model 2022; 62:2869-2879. [PMID: 35594568 DOI: 10.1021/acs.jcim.2c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The three-dimensional conformations of a protein influence its function and select for the ligands it can interact with. The total free energy change during protein-ligand complex formation includes enthalphic and entropic components, which together report on the binding affinity and conformational states of the complex. However, determining the entropic contribution is computationally burdensome. Here, we apply kinematic flexibility analysis (KFA) to efficiently estimate vibrational frequencies from static protein and protein-ligand structures. The vibrational frequencies, in turn, determine the vibrational entropies of the structures and their complexes. Our estimates of the vibrational entropy change caused by ligand binding compare favorably to values obtained from a dynamic Normal Mode Analysis (NMA). Higher correlation factors can be achieved by increasing the distance cutoff in the potential energy model. Furthermore, we apply our new method to analyze the entropy changes of the SARS CoV-2 main protease when binding with different ligand inhibitors, which is relevant for the design of potential drugs.
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Affiliation(s)
- Xiyu Chen
- Institute of Applied Dynamics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Sigrid Leyendecker
- Institute of Applied Dynamics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Henry van den Bedem
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 94720 San Francisco, California, United States
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2
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Liu CW, Kuo BC, Liu MH, Huang YR, Chen CL. Computer simulation for the study of the liquid chromatographic separation of explosive molecules. J Mol Graph Model 2018; 85:331-339. [PMID: 30292170 DOI: 10.1016/j.jmgm.2018.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/17/2018] [Accepted: 09/18/2018] [Indexed: 10/28/2022]
Abstract
The application of high performance liquid chromatography (HPLC) to separate explosive chemicals was investigated by molecular dynamics (MD) simulations. The explosive ingredients including NG, RDX, HMX and TNT were assigned as solutes, while methanol (CH3OH) and acetonitrile (CH3CN) were assigned as solvents in the solution system. The polymeric-molecular siloxanes (SiC8) and poly-1,2-methylenedioxy-4-propenyl benzene (PISAF) compounds were treated as stationary phase in the simulation. The simulation results showed that the different species of explosive ingredients were separated successfully in the solutions by each of the constructed stationary phase of SiC8 and PISAF after a total simulation time of 12.0 ps approximately, which were consistent with the experimental analysis of HPLC spectra. The origin for the separation was found due to the electrostatic interactions between polymer and explosives.
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Affiliation(s)
- Chuan-Wen Liu
- Department of Chemical and Materials Engineering, Chung-Cheng Institute of Technology, National Defense University, Taoyuan, 335, Taiwan, ROC
| | - Bing-Cheng Kuo
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, 804, Taiwan, ROC
| | - Min-Hsien Liu
- Department of Chemical and Materials Engineering, Chung-Cheng Institute of Technology, National Defense University, Taoyuan, 335, Taiwan, ROC
| | - Yu-Ren Huang
- Department of Applied Science, Naval Academy, Zuoying District, Kaohsiung City, 813, Taiwan, ROC
| | - Cheng-Lung Chen
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, 804, Taiwan, ROC.
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3
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Salvalaglio M, Paloni M, Guelat B, Morbidelli M, Cavallotti C. A two level hierarchical model of protein retention in ion exchange chromatography. J Chromatogr A 2015; 1411:50-62. [DOI: 10.1016/j.chroma.2015.07.101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/23/2015] [Accepted: 07/27/2015] [Indexed: 10/23/2022]
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4
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Liang J, Fieg G, Jakobtorweihen S. Ion-Exchange Adsorption of Proteins: Experiments and Molecular Dynamics Simulations. CHEM-ING-TECH 2015. [DOI: 10.1002/cite.201400095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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5
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Liang J, Fieg G, Jakobtorweihen S. Molecular Dynamics Simulations of a Binary Protein Mixture Adsorption onto Ion-Exchange Adsorbent. Ind Eng Chem Res 2015. [DOI: 10.1021/ie504374x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juan Liang
- Institute
of Process and Plant Engineering, Hamburg University of Technology, Schwarzenbergstrasse 95, 21073 Hamburg, Germany
| | - Georg Fieg
- Institute
of Process and Plant Engineering, Hamburg University of Technology, Schwarzenbergstrasse 95, 21073 Hamburg, Germany
| | - Sven Jakobtorweihen
- Institute
of Thermal Separation Processes, Hamburg University of Technology, Eissendorfer Strasse 38, 21073 Hamburg, Germany
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6
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Yu L, Zhang L, Sun Y. Protein behavior at surfaces: Orientation, conformational transitions and transport. J Chromatogr A 2015; 1382:118-34. [DOI: 10.1016/j.chroma.2014.12.087] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/26/2014] [Accepted: 12/31/2014] [Indexed: 12/18/2022]
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7
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Liang J, Fieg G, Keil FJ, Jakobtorweihen S. Adsorption of Proteins onto Ion-Exchange Chromatographic Media: A Molecular Dynamics Study. Ind Eng Chem Res 2012. [DOI: 10.1021/ie301407b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juan Liang
- Institute of Process and Plant Engineering and ‡Institute of
Chemical Reaction Engineering, Hamburg University of Technology, 21073 Hamburg, Germany
| | - Georg Fieg
- Institute of Process and Plant Engineering and ‡Institute of
Chemical Reaction Engineering, Hamburg University of Technology, 21073 Hamburg, Germany
| | - Frerich J. Keil
- Institute of Process and Plant Engineering and ‡Institute of
Chemical Reaction Engineering, Hamburg University of Technology, 21073 Hamburg, Germany
| | - Sven Jakobtorweihen
- Institute of Process and Plant Engineering and ‡Institute of
Chemical Reaction Engineering, Hamburg University of Technology, 21073 Hamburg, Germany
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8
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Lu D, Yang C, Liu Z. How hydrophobicity and the glycosylation site of glycans affect protein folding and stability: a molecular dynamics simulation. J Phys Chem B 2011; 116:390-400. [PMID: 22118044 DOI: 10.1021/jp203926r] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Glycosylation is one of the most common post-translational modifications in the biosynthesis of protein, but its effect on the protein conformational transitions underpinning folding and stabilization is poorly understood. In this study, we present a coarse-grained off-lattice 46-β barrel model protein glycosylated by glycans with different hydrophobicity and glycosylation sites to examine the effect of glycans on protein folding and stabilization using a Langevin dynamics simulation, in which an H term was proposed as the index of the hydrophobicity of glycan. Compared with its native counterpart, introducing glycans of suitable hydrophobicity (0.1 < H < 0.4) at flexible peptide residues of this model protein not only facilitated folding of the protein but also increased its conformation stability significantly. On the contrary, when glycans were introduced at the restricted peptide residues of the protein, only those hydrophilic (H = 0) or very weak hydrophobic (H < 0.2) ones contributed slightly to protein stability but hindered protein folding due to increased free energy barriers. The glycosylated protein retained the two-step folding mechanism in terms of hydrophobic collapse and structural rearrangement. Glycan chains located in a suitable site with an appropriate hydrophobicity facilitated both collapse and rearrangement, whereas others, though accelerating collapse, hindered rearrangement. In addition to entropy effects, that is, narrowing the space of the conformations of the unfolded state, the presence of glycans with suitable hydrophobicity at suitable glycosylation site strengthened the folded state via hydrophobic interaction, that is, the enthalpy effect. The simulations have shown both the stabilization and the destabilization effects of glycosylation, as experimentally reported in the literature, and provided molecular insight into glycosylated proteins. The understanding of the effects of glycans with different hydrophobicities on the folding and stability of protein, as attempted by the present work, is helpful not only to explain the stabilization and destabilization effect of real glycoproteins but also to design protein-polymer conjugates for biotechnological purposes.
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Affiliation(s)
- Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
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Aguilar PP, Nunes CA, Cascalheira JF, Dias-Cabral AC. Kinetics of Angiotensin I alteration of conformation on different hydrophobic interaction chromatographic surfaces. J Chromatogr A 2011; 1218:8322-32. [DOI: 10.1016/j.chroma.2011.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 08/26/2011] [Accepted: 09/07/2011] [Indexed: 10/17/2022]
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10
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Zhang L, Zhao G, Sun Y. Molecular dynamics simulation and experimental validation of the effect of pH on protein desorption in hydrophobic charge induction chromatography. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927022.2010.506511] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Zhang L, Bai S, Sun Y. Molecular dynamics simulation of the effect of ligand homogeneity on protein behavior in hydrophobic charge induction chromatography. J Mol Graph Model 2010; 28:863-9. [DOI: 10.1016/j.jmgm.2010.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 03/07/2010] [Accepted: 03/14/2010] [Indexed: 11/26/2022]
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12
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Zhang L, Sun Y. Molecular simulation of adsorption and its implications to protein chromatography: A review. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2009.12.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Zhang L, Zhao G, Sun Y. Effects of Ligand Density on Hydrophobic Charge Induction Chromatography: Molecular Dynamics Simulation. J Phys Chem B 2010; 114:2203-11. [DOI: 10.1021/jp903852c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lin Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Guofeng Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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14
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Zhang L, Zhao G, Sun Y. Molecular Insight into Protein Conformational Transition in Hydrophobic Charge Induction Chromatography: A Molecular Dynamics Simulation. J Phys Chem B 2009; 113:6873-80. [DOI: 10.1021/jp809754k] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lin Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Guofeng Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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