Computational analysis of membrane proteins: the largest class of drug targets

Y Arinaminpathy, E Khurana, DM Engelman… - Drug discovery today, 2009 - Elsevier
Given the key roles of integral membrane proteins as transporters and channels, it is
necessary to understand their structures and, hence, mechanisms and regulation at the …

Molecular dynamics simulations of proteins in lipid bilayers

J Gumbart, Y Wang, A Aksimentiev… - Current opinion in …, 2005 - Elsevier
With recent advances in X-ray crystallography of membrane proteins promising many new
high-resolution structures, molecular dynamics simulations will become increasingly …

Computational modeling of ion transport through nanopores

N Modi, M Winterhalter, U Kleinekathöfer - Nanoscale, 2012 - pubs.rsc.org
Nanoscale pores are ubiquitous in biological systems while artificial nanopores are being
fabricated for an increasing number of applications. Biological pores are responsible for the …

Advances in enhanced sampling molecular dynamics simulations for biomolecules

A Wang, Z Zhang, G Li - Chinese Journal of Chemical Physics, 2019 - pubs.aip.org
Molecular dynamics simulation has emerged as a powerful computational tool for studying
biomolecules as it can provide atomic insights into the conformational transitions involved in …

The conformational transition pathway of ATP binding cassette transporter MsbA revealed by atomistic simulations

JW Weng, KN Fan, WN Wang - Journal of Biological Chemistry, 2010 - ASBMB
ATP binding cassette transporters are integral membrane proteins that use the energy
released from ATP hydrolysis at the two nucleotide binding domains (NBDs) to translocate a …

The role of the interdomain interactions on RfaH dynamics and conformational transformation

JB Gc, BS Gerstman, PP Chapagain - The journal of physical …, 2015 - ACS Publications
The transcription antiterminator RfaH has been shown to undergo major structural
rearrangements to perform multiple functions. Structural determination of the C-terminal …

Probing the energy landscape of activation gating of the bacterial potassium channel KcsA

T Linder, BL de Groot… - PLOS Computational …, 2013 - journals.plos.org
The bacterial potassium channel KcsA, which has been crystallized in several
conformations, offers an ideal model to investigate activation gating of ion channels. In this …

Modeling HERG and its interactions with drugs: recent advances in light of current potassium channel simulations

M Recanatini, A Cavalli… - … : Chemistry Enabling Drug …, 2008 - Wiley Online Library
The hERG K+ channel is responsible for the rapid delayed rectifier current in cardiac
myocytes, and a block of its functioning may be related with the (inherited or drug‐induced) …

Molecular insight into conformational transmission of human P-glycoprotein

SY Chang, FF Liu, XY Dong, Y Sun - The Journal of chemical physics, 2013 - pubs.aip.org
P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates
through a channel at the two transmembrane domains (TMDs) across the cell membranes …

Ion hydration in nanopores and the molecular basis of selectivity

M Carrillo-Tripp, ML San-Román… - Biophysical …, 2006 - Elsevier
Using a simple model, it is shown that the cost of constraining a hydrated potassium ion
inside a narrow pore is smaller than the cost of constraining hydrated sodium or lithium ions …