Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

T Mori, N Miyashita, W Im, M Feig, Y Sugita - Biochimica et Biophysica Acta …, 2016 - Elsevier
This paper reviews various enhanced conformational sampling methods and explicit/implicit
solvent/membrane models, as well as their recent applications to the exploration of the …

Transmembrane signal transduction by peptide hormones via family BG protein-coupled receptors

KJ Culhane, Y Liu, Y Cai, ECY Yan - Frontiers in pharmacology, 2015 - frontiersin.org
Although family BG protein-coupled receptors (GPCRs) contain only 15 members, they play
key roles in transmembrane signal transduction of hormones. Family B GPCRs are drug …

Receptor activity-modifying protein-directed G protein signaling specificity for the calcitonin gene-related peptide family of receptors

C Weston, I Winfield, M Harris, R Hodgson… - Journal of Biological …, 2016 - ASBMB
The calcitonin gene-related peptide (CGRP) family of G protein-coupled receptors (GPCRs)
is formed through the association of the calcitonin receptor-like receptor (CLR) and one of …

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 …

Molecular Insights into Phosphorylation-Induced Allosteric Conformational Changes in a β2-Adrenergic Receptor

MK Madhu, A Debroy, RK Murarka - The Journal of Physical …, 2022 - ACS Publications
The large conformational flexibility of G protein-coupled receptors (GPCRs) has been a
puzzle in structural and pharmacological studies for the past few decades. Apart from …

Integrating multiple accelerated molecular dynamics to improve accuracy of free energy calculations

X Peng, Y Zhang, Y Li, QL Liu, H Chu… - Journal of Chemical …, 2018 - ACS Publications
Accelerated Molecular Dynamics (aMD) is a promising enhanced sampling method to
explore the conformational space of biomolecules. However, the large statistical noise in …

[HTML][HTML] Receptor activity-modifying protein dependent and independent activation mechanisms in the coupling of calcitonin gene-related peptide and adrenomedullin …

MJ Woolley, CA Reynolds, J Simms, CS Walker… - Biochemical …, 2017 - Elsevier
Calcitonin gene-related peptide (CGRP) or adrenomedullin (AM) receptors are heteromers
of the calcitonin receptor-like receptor (CLR), a class BG protein-coupled receptor, and one …

Development of covalent inhibitors: Principle, design, and application in cancer

L Zheng, Y Li, D Wu, H Xiao, S Zheng… - MedComm …, 2023 - Wiley Online Library
Covalent inhibitors have been a rapidly growing field in drug discovery due to their
therapeutic potential and unique advantages in cancer therapy. As opposed to noncovalent …

Biased Signaling in Mutated Variants of β2-Adrenergic Receptor: Insights from Molecular Dynamics Simulations

MK Madhu, K Shewani, RK Murarka - Journal of Chemical …, 2024 - ACS Publications
The molecular basis of receptor bias in G protein-coupled receptors (GPCRs) caused by
mutations that preferentially activate specific intracellular transducers over others remains …

Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins

T Yasuda, R Morita, Y Shigeta… - Journal of Chemical …, 2022 - ACS Publications
Free energy landscapes (FELs) of proteins are indispensable for evaluating thermodynamic
properties. Molecular dynamics (MD) simulation is a computational method for calculating …