Computational analysis of membrane proteins: the largest class of drug targets
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 …
necessary to understand their structures and, hence, mechanisms and regulation at the …
Molecular dynamics simulations of proteins in lipid bilayers
With recent advances in X-ray crystallography of membrane proteins promising many new
high-resolution structures, molecular dynamics simulations will become increasingly …
high-resolution structures, molecular dynamics simulations will become increasingly …
Computational modeling of ion transport through nanopores
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 …
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 …
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 …
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
The transcription antiterminator RfaH has been shown to undergo major structural
rearrangements to perform multiple functions. Structural determination of the C-terminal …
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 …
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
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) …
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 …
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 …
inside a narrow pore is smaller than the cost of constraining hydrated sodium or lithium ions …