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Title: Computational approaches to detect allosteric pathways in transmembrane molecular machines

Journal Article · · Biochimica et Biophysica Acta. Biomembranes

Sponsoring Organization:
USDOE
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231
OSTI ID:
1367693
Alternate ID(s):
OSTI ID: 1326419
Journal Information:
Biochimica et Biophysica Acta. Biomembranes, Journal Name: Biochimica et Biophysica Acta. Biomembranes Vol. 1858 Journal Issue: 7 PB; ISSN 0005-2736
Publisher:
ElsevierCopyright Statement
Country of Publication:
Netherlands
Language:
English
Citation Metrics:
Cited by: 43 works
Citation information provided by
Web of Science

References (99)

X-ray structures of LeuT in substrate-free outward-open and apo inward-open states journal January 2012
A comparison of techniques for calculating protein essential dynamics journal January 1997
Satisfying Hydrogen Bonding Potential in Proteins journal May 1994
AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems journal May 2015
Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser journal July 2015
The Signaling Pathway of Rhodopsin journal May 2007
Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs journal October 2013
Analyzing and visualizing residue networks of protein structures journal April 2011
The Glutamate-Activated Anion Conductance in Excitatory Amino Acid Transporters Is Gated Independently by the Individual Subunits journal March 2007
Unlocking the molecular secrets of sodium-coupled transporters journal May 2009
Network Analysis of Protein Structures Identifies Functional Residues journal December 2004
Activation mechanism of the  2-adrenergic receptor journal October 2011
The changing landscape of protein allostery journal February 2006
Structure of a glutamate transporter homologue from Pyrococcus horikoshii journal October 2004
Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone journal September 2011
Allosteric pathways in imidazole glycerol phosphate synthase journal May 2012
Ion-Controlled Conformational Dynamics in the Outward-Open Transition from an Occluded State of LeuT journal September 2012
Is allostery an intrinsic property of all dynamic proteins? journal July 2004
G Protein–Coupled Receptor Oligomerization Revisited: Functional and Pharmacological Perspectives journal February 2014
o GNM: online computation of structural dynamics using the Gaussian Network Model journal July 2006
Elastic network normal mode dynamics reveal the GPCR activation mechanism: Normal Modes of GPCR journal October 2013
Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations journal November 1991
Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities journal November 2012
Evolutionarily conserved networks of residues mediate allosteric communication in proteins journal December 2002
Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families journal October 1999
Allosteric modulation of G protein-coupled receptors: A pharmacological perspective journal January 2011
Chapter 2 Quantifying Uncertainty and Sampling Quality in Biomolecular Simulations book January 2009
Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles journal August 2009
Activation and allosteric modulation of a muscarinic acetylcholine receptor journal November 2013
Allosteric sodium in class A GPCR signaling journal May 2014
Network analysis of protein dynamics journal May 2007
A Model for the Topology of Excitatory Amino Acid Transporters Determined by the Extracellular Accessibility of Substituted Cysteines journal March 2000
Biased Agonism at G Protein-Coupled Receptors: The Promise and the Challenges-A Medicinal Chemistry Perspective: BIASED AGONISM AT G PROTEIN-COUPLED RECEPTORS journal May 2014
Allostery without a conformational change? Revisiting the paradigm journal February 2015
Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations journal August 2009
Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits * journal January 1966
xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures. journal June 2012
Substrate-modulated gating dynamics in a Na+-coupled neurotransmitter transporter homologue journal April 2011
Single-molecule dynamics of gating in a neurotransmitter transporter homologue journal May 2010
Structural Intermediates in a Model of the Substrate Translocation Path of the Bacterial Glutamate Transporter Homologue GltPh journal April 2012
Finding and evaluating community structure in networks journal February 2004
Essential dynamics of proteins journal December 1993
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential journal June 1997
Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors journal August 2010
PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins journal April 2014
Shedding light on protein–ligand binding by graph theory: The topological nature of allostery journal May 2012
NetworkView: 3D display and analysis of protein{middle dot}RNA interaction networks journal September 2012
Crystal structure of an asymmetric trimer of a bacterial glutamate transporter homolog journal February 2012
Mechanism of the Association between Na + Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters journal April 2015
Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis journal January 2014
Transport mechanism of a bacterial homologue of glutamate transporters journal November 2009
Principles of protein-protein interactions. journal January 1996
A Mathematical Theory of Communication journal July 1948
Exploring Residue Component Contributions to Dynamical Network Models of Allostery journal July 2012
Simple Allosteric Model for Membrane Pumps journal August 1966
Protein-protein interaction at crystal contacts journal December 1995
Atomic-Level Characterization of the Structural Dynamics of Proteins journal October 2010
Sampling and statistics in biomolecular simulations
  • Sim, Hoon; Diraviyam, Karthikeyan; Saxena, Akansha
  • THEORY AND APPLICATIONS IN COMPUTATIONAL CHEMISTRY: THE FIRST DECADE OF THE SECOND MILLENNIUM: International Congress TACC-2012, AIP Conference Proceedings https://doi.org/10.1063/1.4730657
conference January 2012
Spontaneous Inward Opening of the Dopamine Transporter Is Triggered by PIP 2 -Regulated Dynamics of the N-Terminus journal August 2015
Dimerization and ligand binding affect the structure network of A2A adenosine receptor journal May 2011
SLC6 Neurotransmitter Transporters: Structure, Function, and Regulation journal July 2011
A Specific Cholesterol Binding Site Is Established by the 2.8 Å Structure of the Human β2-Adrenergic Receptor journal June 2008
Crystal structure of the human β2 adrenergic G-protein-coupled receptor journal October 2007
Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters journal July 2005
Allosteric Effects of Sodium Ion Binding on Activation of the M3 Muscarinic G-Protein-Coupled Receptor journal April 2015
A Competitive Inhibitor Traps LeuT in an Open-to-Out Conformation journal December 2008
Constraints Imposed by the Membrane Selectively Guide the Alternating Access Dynamics of the Glutamate Transporter GltPh journal March 2012
A Role for Information Collection, Management, and Integration in Structure-Function Studies of G-Protein Coupled Receptors journal May 2006
Generalized correlation for biomolecular dynamics journal December 2005
Allosteric Mechanisms of Molecular Machines at the Membrane: Transport by Sodium-Coupled Symporters journal February 2016
Intersubunit Interactions in EAAT4 Glutamate Transporters journal July 2006
The Mechanism of a Neurotransmitter:Sodium Symporter—Inward Release of Na+ and Substrate Is Triggered by Substrate in a Second Binding Site journal June 2008
A new mechanism of allostery in a G protein–coupled receptor dimer journal August 2014
Conformational Spread: The Propagation of Allosteric States in Large Multiprotein Complexes journal June 2004
Structure of a nanobody-stabilized active state of the β2 adrenoceptor journal January 2011
Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis journal August 1996
Conserved amino acids participate in the structure networks deputed to intramolecular communication in the lutropin receptor journal September 2010
Transport domain unlocking sets the uptake rate of an aspartate transporter journal February 2015
Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins journal March 2010
Emerging paradigms in GPCR allostery: implications for drug discovery journal August 2013
Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter:sodium symporters journal June 2010
Crystal structure of the β2 adrenergic receptor–Gs protein complex journal July 2011
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations journal July 1983
Sodium Ion Binding Pocket Mutations and Adenosine A 2A Receptor Function journal December 2014
NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT journal May 2014
Building-block approach for determining low-frequency normal modes of macromolecules journal January 2000
A Coarse-Grained Normal Mode Approach for Macromolecules:An Efficient Implementation and Application to Ca2+-ATPase journal November 2002
Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter journal January 2007
Activation and dynamic network of the M2 muscarinic receptor journal June 2013
Individual Subunits of the Glutamate Transporter EAAC1 Homotrimer Function Independently of Each Other journal September 2005
A Functional Selectivity Mechanism at the Serotonin-2A GPCR Involves Ligand-Dependent Conformations of Intracellular Loop 2 journal October 2014
On the nature of allosteric transitions: A plausible model journal May 1965
Dynamical networks in tRNA:protein complexes journal April 2009
On the calculation of entropy from covariance matrices of the atomic fluctuations journal October 2001
Functional Selectivity and Classical Concepts of Quantitative Pharmacology journal June 2006
The ensemble nature of allostery journal April 2014
An Intracellular Interaction Network Regulates Conformational Transitions in the Dopamine Transporter journal April 2008
What Can Crystal Structures of Aminergic Receptors Tell Us about Designing Subtype-Selective Ligands? journal December 2014
Structural basis for Na + -sensitivity in dopamine D2 and D3 receptors journal January 2015

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