Conformational transitions of adenylate kinase: switching by cracking.

No abstract is available for this paper.

• Publication year

  2007

• Venue

  Journal of Molecular Biology

• Publication date

  2007-03-09

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1016/J.JMB.2006.11.085PMID 17217965PMCID PMC2561047
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions.

  2009cited by this paper
• The changing landscape of protein allostery.

  2006cited by this paper
• Topological frustration and the folding of interleukin-1 beta.

  2006cited by this paper
• Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

  2006cited by this paper
• Mechanisms of protein assembly: lessons from minimalist models.

  2006cited by this paper
• Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery.

  2005cited by this paper
• A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes.

  2005cited by this paper
• Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor.

  2005cited by this paper
• Simple energy landscape model for the kinetics of functional transitions in proteins.

  2005cited by this paper
• Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase.

  2005cited by this paper
• Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode‐coupling 15N‐NMR relaxation data

  2004cited by this paper
• Domain swapping is a consequence of minimal frustration.

  2004cited by this paper
• Associative mechanism for phosphoryl transfer: A molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates

  2004cited by this paper
• Catalytic Domain Crystal Structure of Protein Kinase C-θ (PKCθ)*♦

  2004cited by this paper
• Is allostery an intrinsic property of all dynamic proteins?

  2004cited by this paper
• Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates.

  2004cited by this paper
• Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair

  2004cited by this paper
• Simulation of an Ensemble of Conformational Transitions in a United-Residue Model of Calmodulin

  2004cited by this paper
• Theory of protein folding.

  2004cited by this paper
• Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

  2003influential reference
• The role of dynamics in allosteric regulation.

  2003cited by this paper
• Enzyme Dynamics During Catalysis

  2002cited by this paper
• Structure of the Carboxyl-terminal Src Kinase, Csk*

  2002cited by this paper
• Anisotropy of fluctuation dynamics of proteins with an elastic network model.

  2001influential reference
• Prediction of folding mechanism for circular-permuted proteins.

  2001cited by this paper
• Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

  2000cited by this paper
• Folding funnels, binding funnels, and protein function

  1999cited by this paper
• Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding

  1999cited by this paper
• Folding funnels and frustration in off-lattice minimalist protein landscapes.

  1998cited by this paper
• Structural correlations in protein folding funnels.

  1997cited by this paper
• Domain closure in adenylate kinase.

  1996cited by this paper
• Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding.

  1996cited by this paper
• Molecular docking using surface complementarity

  1996cited by this paper
• VMD: visual molecular dynamics.

  1996cited by this paper
• Funnels, pathways, and the energy landscape of protein folding: A synthesis

  1994cited by this paper
• Crystal structure of cyclin-dependent kinase 2

  1993cited by this paper
• Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state.

  1992cited by this paper
• Protein folding funnels: a kinetic approach to the sequence-structure relationship.

  1992cited by this paper
• Optimized Monte Carlo data analysis.

  1989cited by this paper
• New Monte Carlo technique for studying phase transitions.

  1988cited by this paper
• Spin glasses and the statistical mechanics of protein folding.

  1987cited by this paper
• Molecular dynamics with coupling to an external bath

  1984cited by this paper
• Rapid comparison of protein structures

  1982cited by this paper
• Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions.

  1975cited by this paper

• Hydrophobic interactions determine the optimum temperature of a housekeeping enzyme.

  2026cites this paper
• Protein Language Models and Structure-Based Machine Learning for Prediction of Allosteric Binding Sites in Protein Kinases: An Explainable AI Framework Grounded in Energy Landscape-Encoded Frustration

  2026cites this paper
• Role of mechanical allostery in kindlin-mediated integrin activation

  2026cites this paper
• Simulating biomolecules for physiological timescales.

  2025cites this paper
• Contact networks encode the ATP-induced dynamic structural asymmetry of condensin head domains.

  2025cites this paper
• k-Nearest Neighbor Adaptive Sampling, a Simple Tool to Efficiently Explore Conformational Space.

  2025cites this paper
• Dynamic energy conversion in protein catalysis: From brownian motion to enzymatic function

  2025influential citation
• Exploring Helical Fraying Linked to Dynamics and Catalysis in Adenylate Kinase

  2025cites this paper
• Allosteric Regulation of Enzymatic Catalysis through Mechanical Force.

  2025cites this paper
• Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations

  2025cites this paper
• Multiple-Basin Go̅-Martini for Investigating Conformational Transitions and Environmental Interactions of Proteins

  2025cites this paper
• Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome

  2025cites this paper
• Cracking Controls ATP Hydrolysis in the catalytic unit of a P-type ATPase

  2025cites this paper
• Interplay between conformational dynamics and substrate binding regulates enzymatic activity: a single-molecule FRET study

  2025cites this paper
• Allostery can convert binding free energies into concerted domain motions in enzymes

  2024cites this paper
• Associating protein sequence positions with the modulation of quantitative phenotypes.

  2024cites this paper
• Towards the understanding of molecular motors and its relationship with local unfolding

  2024influential citation
• A contact‐based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold‐switch

  2024cites this paper
• GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models

  2024cites this paper
• Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase.

  2024cites this paper
• NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function.

  2024cites this paper
• Explaining Conformational Diversity in Protein Families through Molecular Motions

  2024cites this paper
• Conformational dynamics of adenylate kinase in crystals

  2024cites this paper
• Accurate Characterization of Binding Kinetics and Allosteric Mechanisms for the HSP90 Chaperone Inhibitors Using AI-Augmented Integrative Biophysical Studies

  2024cites this paper
• Enzyme activation by urea reveals the interplay between conformational dynamics and substrate binding: a single-molecule FRET study

  2024cites this paper
• Skipping events impose repeated binding attempts: profound kinetic implications of protein–DNA conformational changes

  2024cites this paper
• PhISCO: a simple method to infer phenotypes from protein sequences

  2023cites this paper
• A highly efficient human cell-free translation system

  2023cites this paper
• Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase

  2023cites this paper
• Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models

  2023cites this paper
• A highly efficient human cell-free translation system

  2023cites this paper
• Protein dynamics: The future is bright and complicated!

  2023cites this paper
• The energy landscape of the ribosome

  2023cites this paper
• Bidirectional allostery mechanism of catch-bond effect in cell adhesion

  2023cites this paper
• Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release

  2023cites this paper
• Mechanism and design of allosteric activators of SIRT1

  2022cites this paper
• Role of Repeated Conformational Transitions in Substrate Binding of Adenylate Kinase

  2022cites this paper
• The role of C-terminal helix in the conformational transition of an arginine binding protein

  2022cites this paper
• Integration of Adenylate Kinase 1 with Its Peptide Conformational Imprint

  2022cites this paper
• Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology

  2022cites this paper
• Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins

  2022cites this paper
• Csk αC Helix: A Computational Analysis of an Essential Region for Conformational Transitions.

  2022cites this paper
• A hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data

  2022cites this paper
• Developing and Implementing Cloud-Based Tutorials That Combine Bioinformatics Software, Interactive Coding, and Visualization Exercises for Distance Learning on Structural Bioinformatics

  2021cites this paper
• Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins

  2021cites this paper
• Role of Calcium in Modulating the Conformational Landscape and Peptide Binding Induced Closing of Calmodulin.

  2021cites this paper
• Assessing the Interactions of Statins with Human Adenylate Kinase Isoenzyme 1: Fluorescence and Enzyme Kinetic Studies

  2021cites this paper
• Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics

  2021cites this paper
• Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains.

  2021cites this paper
• Physics of biomolecular recognition and conformational dynamics

  2021cites this paper
• Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion

  2021cites this paper
• Impacts of mutations on dynamic allostery of adenylate kinase.

  2021cites this paper
• Tracking the ATP-binding response in adenylate kinase in real time

  2021cites this paper
• Dynamic particle swarm optimization of biomolecular simulation parameters with flexible objective functions

  2021cites this paper
• Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.

  2021cites this paper
• SMOG 2 and OpenSMOG: Extending the limits of structure-based models

  2021cites this paper
• A graph-based algorithm for detecting rigid domains in protein structures

  2021cites this paper
• Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase

  2020cites this paper
• Mechanistic basis for motor-driven membrane constriction by dynamin

  2020cites this paper
• Using multiscale molecular dynamics simulations to obtain insights into pore forming toxin mechanisms.

  2020cites this paper
• An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules

  2020cites this paper
• Computational Studies of Enzyme Motions

  2020cites this paper
• Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics

  2020cites this paper
• Binding-Induced Conformational Changes Involved in Sliding Clamp PCNA and DNA Polymerase DPO4

  2020cites this paper
• A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs

  2020cites this paper
• Experimental insight into enzyme catalysis and dynamics: A review on applications of state of art spectroscopic methods.

  2020cites this paper
• Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins

  2020cites this paper
• A Two-ended DAta-Driven Accelerated Sampling Method for Exploring the Transition Pathways between Two Known States of Protein.

  2020cites this paper
• Probing surface accessibility in the dynamic meshwork of protein-protein interactions.

  2020cites this paper
• Physiological and proteomic responses of mangrove plant Avicennia marina seedlings to simulated periodical inundation

  2020cites this paper
• Hydrogen deuterium exchange defines catalytically linked regions of protein flexibility in the catechol O-methyltransferase reaction

  2020cites this paper
• Role of substrate-product frustration on enzyme functional dynamics.

  2019cites this paper
• Multiscale landscape of molecular mechanism of SIRT1 activation by STACs.

  2019cites this paper
• Family permutation profiling identifies a dynamic protein domain as functionally tolerant to increased conformational entropy

  2019cites this paper
• Successes and challenges in simulating the folding of large proteins

  2019cites this paper
• Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance Ratio

  2019cites this paper
• Redesigning N-glycosylation sites in a GH3 β-xylosidase improves the enzymatic efficiency

  2019cites this paper
• Exploring and Engineering the Conformational Landscape of Calmodulin through Specific Interactions.

  2019cites this paper
• Dissecting the energetics of subunit rotation in the ribosome

  2019cites this paper
• Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts.

  2019influential citation
• Rapid interpretation of small-angle X-ray scattering data

  2019cites this paper
• Studying ribosome dynamics with simplified models.

  2019cites this paper
• Unsupervised Graph-Based Learning Predicts Mutations That Alter Protein Dynamics

  2019cites this paper
• Protein conformational transitions coupling with ligand interactions: Simulations from molecules to medicine

  2019cites this paper
• Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level

  2019cites this paper
• Stability and Strain in Hisactophilin and Mechanism of the Myristoyl Switch

  2019cites this paper
• Searching for the origin of protein conformational changes: Protein responses to specific forces in simulations

  2019cites this paper
• Conformational state switching and pathways of chromosome dynamics in cell cycle

  2019cites this paper
• Nature's Shortcut to Protein Folding.

  2019cites this paper
• Overcoming the Bottleneck of the Enzymatic Cycle by Steric Frustration.

  2019cites this paper
• Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations

  2019cites this paper
• Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open–Closed Transition

  2018cites this paper
• Multiple Pathways and Time Scales for Conformational Transitions in apo-Adenylate Kinase.

  2018cites this paper
• Mechanochemical Model of the Power Stroke of the Single-Headed Motor Protein KIF1A.

  2018cites this paper
• Exploration of Multistate Conformational Dynamics upon Ligand Binding of a Monomeric Enzyme Involved in Pyrophosphoryl Transfer.

  2018cites this paper
• Using Spectral Representation to Classify Proteins’ Conformational States

  2018cites this paper
• Rotation-Activated and Cooperative Zipping Characterize Class I Viral Fusion Protein Dynamics.

  2018cites this paper
• Disorder guides domain rearrangement in elongation factor Tu

  2018cites this paper
• Differential Enzyme Flexibility Probed Using Solid-State Nanopores.

  2018cites this paper
• Simulations Reveal Multiple Intermediates in the Unzipping Mechanism of Neuronal SNARE Complex.

  2018cites this paper