NDLI: Protein Surface Dynamics: Interaction with Water and Small Solutes

Content Provider	Springer Nature Link
Author	Friedman, Ran Nachliel, Esther Gutman, Menachem
Copyright Year	2005
Abstract	Previous time resolved measurements had indicated that protons could propagate on the surface of a protein, or a membrane, by a special mechanism that enhances the shuttle of the proton towards a specific site [1]. It was proposed that a proper location of residues on the surface contributes to the proton shuttling function. In the present study, this notion was further investigated using molecular dynamics, with only the mobile charge replaced by Na$^{+}$ and Cl$^{−}$ ions. A molecular dynamics simulation of a small globular protein (the S6 of the bacterial ribosome) was carried out in the presence of explicit water molecules and four pairs of Na$^{+}$ and Cl$^{−}$ ions. A 10 ns simulation indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. Yet it was noted that, close to some domains, the ions extended their duration near the surface, suggesting that the local electrostatic potential prevented them from diffusing to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.
Starting Page	433
Ending Page	452
Page Count	20
File Format	PDF
ISSN	00920606
Journal	Journal of Biological Physics
Volume Number	31
Issue Number	3-4
e-ISSN	15730689
Language	English
Publisher	Kluwer Academic Publishers
Publisher Date	2005-01-01
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	molecular dynamics ions at interface protein-salt interactions Neurosciences Bioinformatics Polymer Sciences Statistical Physics Condensed Matter Biophysics/Biomedical Physics
Content Type	Text
Resource Type	Article
Subject	Cell Biology Atomic and Molecular Physics, and Optics Molecular Biology Biophysics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Protein surface dynamics: interaction with water and small solutes.

Instrument-Dependent Cadherin Monolayer Interactions

A Physical Picture of Protein Dynamics and Conformational Changes

Protein Structure from X-Ray Diffraction

Protein Surface Dynamics: Interaction with Water and Small Solutes

Energy Landscape and Dynamics of Biomolecules Extended Abstract

Contents Volume 29 (2003)

Physics of Ion Channels

Water and Protein Movements in Ligand-Receptor Interactions

Protein Surface Dynamics: Interaction with Water and Small Solutes

Similar Documents

Protein surface dynamics: interaction with water and small solutes.

Instrument-Dependent Cadherin Monolayer Interactions

A Physical Picture of Protein Dynamics and Conformational Changes

Protein Structure from X-Ray Diffraction

Protein Surface Dynamics: Interaction with Water and Small Solutes

Energy Landscape and Dynamics of Biomolecules Extended Abstract

Contents Volume 29 (2003)

Physics of Ion Channels

Water and Protein Movements in Ligand-Receptor Interactions

Protein Surface Dynamics: Interaction with Water and Small Solutes