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您的检索式：作者名="Shawn Witham"
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| 1 | In Silico Investigation of pH-Dependence of Prolactin and Human Growth Hormone Binding to Human Prolactin Receptor显示文摘Experimental data shows that the binding of human prolactin(hPRL)to human prolactin receptor(hPRLr-ECD)is strongly pH-dependent,while the binding of the same receptor to human growth hormone(hGH)is pH-independent.Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids.It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy.Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that the main reason for pH-dependence of the binding of hPRL-hPRLr-ECD is a number of salt-bridges across the interface of the complex,while no salt-bridges are formed in the hGH-hPRlr-ECD.Specifically,most of the salt-bridges involve histidine residues and this is the reason for the pH-dependence across a physiological range of pH.The analysis not only revealed the molecular mechanism of the pH-dependence of the hPRL-hPRLr-ECD,but also provided critical insight into the underlying physicchemical mechanism. | Lin Wang Shawn Witham Zhe Zhang Lin Li Michael Hodsdon Emil Alexov | 2013 | Communications in Computational Physics2013，13，1： | 0 |
| 2 | DelPhi Web Server:A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes显示文摘Here we report a web server,the DelPhi web server,which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions,and dielectric map.The server provides extra services to fix structural defects,as missing atoms in the structural file and allows for generation of missing hydrogen atoms.The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22,Amber98 or OPLS.Upon completion of the calculations,the user is given option to download fixed and protonated structural file,together with the parameter and Delphi output files for further analysis.Utilizing Jmol viewer,the user can see the corresponding structural file,to manipulate it and to change the presentation.In addition,if the potential map is requested to be calculated,the potential can be mapped onto the molecule surface.The DelPhi web server is available from http://gffzzde59a5d64e5c401ehv6w9qkv65qkn65vv.ffgz.tsg.suse.edu.cn/delphi webserver. | Subhra Sarkar Shawn Witham Jie Zhang Maxim Zhenirovskyy Walter Rocchia Emil Alexov | 2013 | Communications in Computational Physics2013，13，1： | 0 |
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