Structural mechanisms for domain movements in proteins.

No abstract is available for this paper.

• Publication year

  1994

• Venue

  Biochemistry

• Publication date

  1994-06-07

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1021/BI00188A001PMID 8204609
• 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.

• A "helix-scissors" mechanism for the hinge-bending conformational change in phosphoglycerate kinase.

  2009cited by this paper
• Simulation of enzyme–substrate encounter with gated active sites

  1994cited by this paper
• Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding.

  1994cited by this paper
• Solution structure of a calmodulin-target peptide complex by multidimensional NMR.

  1994cited by this paper
• Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand.

  1994cited by this paper
• The 2.2 A crystal structure of transducin-alpha complexed with GTP gamma S.

  1994cited by this paper
• Crystal structure of a yeast TBP/TATA-box complex

  1993cited by this paper
• Rat annexin V crystal structure: Ca(2+)-induced conformational changes.

  1993cited by this paper
• The mechanism of iron uptake by transferrins: the structure of an 18 kDa NII-domain fragment from duck ovotransferrin at 2.3 A resolution.

  1993cited by this paper
• The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation.

  1993cited by this paper
• Crystal structure of active elongation factor Tu reveals major domain rearrangements

  1993cited by this paper
• Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces.

  1993cited by this paper
• Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme.

  1993cited by this paper
• The 2.2 Å crystal structure of transducin-α complexed with GTPγS

  1993cited by this paper
• Co-crystal structure of TBP recognizing the minor groove of a TATA element

  1993cited by this paper
• Crystal structure of yeast TATA-binding protein and model for interaction with DNA.

  1993cited by this paper
• Three-dimensional structure of myosin subfragment-1: a molecular motor.

  1993cited by this paper
• Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA.

  1993cited by this paper
• Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.

  1993cited by this paper
• Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation.

  1993cited by this paper
• Modulation of calmodulin plasticity in molecular recognition on the basis of x-ray structures.

  1993cited by this paper
• Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7-A resolution: conformational changes induced by decarboxylation of isocitrate.

  1993cited by this paper
• Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers.

  1993cited by this paper
• The crystal structure of a new high-calcium form of annexin V.

  1993cited by this paper
• Structure of a hinge-bending bacteriophage T4 lysozyme mutant, Ile3-->Pro.

  1993cited by this paper
• Three-dimensional structure of the elastase of Pseudomonas aeruginosa at 1.5-A resolution.

  1993cited by this paper
• Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex.

  1992cited by this paper
• Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis.

  1992cited by this paper
• Crystal structure of the binary complex of pig muscle phosphoglycerate kinase and its substrate 3‐phospho‐D‐glycerate

  1992cited by this paper
• Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor.

  1992cited by this paper
• Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins.

  1992cited by this paper
• Domain closure in mitochondrial aspartate aminotransferase.

  1992cited by this paper
• Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site

  1992cited by this paper
• Catalysis at the interface: the anatomy of a conformational change in a triglyceride lipase.

  1992cited by this paper
• Structural basis of latency in plasminogen activator inhibitor-1

  1992cited 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
• Domain flexibility in aspartic proteinases

  1992cited by this paper
• Structural comparison suggests that thermolysin and related neutral proteases undergo hinge-bending motion during catalysis.

  1992cited by this paper
• The 2.3-A resolution structure of the maltose- or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis.

  1992cited by this paper
• Structure of a recombinant calmodulin from Drosophila melanogaster refined at 2.2-A resolution.

  1992cited by this paper
• Serpin tertiary structure transformation.

  1991cited by this paper
• To build an enzyme....

  1991cited by this paper
• Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase.

  1991cited by this paper
• The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 A resolution.

  1991cited by this paper
• Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase.

  1991influential reference
• The energy landscapes and motions of proteins.

  1991cited by this paper
• Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-A resolution.

  1991cited by this paper
• Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70-kDa heat shock cognate protein.

  1991cited by this paper
• The crystal structure of the “open” and the “closed” conformation of the flexible loop of trypanosomal triosephosphate isomerase

  1991cited by this paper
• Comparison of the periplasmic receptors for L-arabinose, D-glucose/D-galactose, and D-ribose. Structural and Functional Similarity.

  1991cited by this paper
• Mechanism of enolase: the crystal structure of enolase-Mg2(+)-2-phosphoglycerate/phosphoenolpyruvate complex at 2.2-A resolution.

  1991cited by this paper
• Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis.

  1990cited by this paper
• Induced-fit movements in adenylate kinases.

  1990cited by this paper
• A mutant T4 lysozyme displays five different crystal conformations

  1990cited by this paper
• Structural and serological evidence for a novel mechanism of antigenic variation in foot-and-mouth disease virus

  1990cited by this paper
• Apolactoferrin structure demonstrates ligand-induced conformational change in transferrins

  1990cited by this paper
• Three-dimensional structure of the ATPase fragment of a 70K heat-shock cognate protein

  1990cited by this paper
• Time-resolved X-ray crystallographic study of the conformational change in Ha-Ras p21 protein on GTP hydrolysis

  1990cited by this paper
• Plastic adaptation toward mutations in proteins: Structural comparison of thymidylate synthases

  1990cited by this paper
• Modeling the intact form of the alpha 1-proteinase inhibitor.

  1990cited by this paper
• Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate.

  1990cited by this paper
• High specificity of a phosphate transport protein determined by hydrogen bonds

  1990cited by this paper
• Induced-fit movements in adenylate kinases.

  1990cited by this paper
• Three-dimensional structure of the complex of guanylate kinase from yeast with its substrate GMP.

  1990cited by this paper
• Atomic structure of the actin: DNase I complex

  1990cited by this paper
• Molecular dynamics study of secondary structure motion in proteins: Application to myohemerythrin

  1990cited by this paper
• Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop.

  1990cited by this paper
• Modeling the intact form of the α1-proteinase inhibitor

  1990cited by this paper
• High‐resolution X‐ray studies on rabbit serum transferrin: preliminary structure analysis of the N‐terminal half‐molecule at 2.3 Å resolution

  1990cited by this paper
• Periplasmic binding protein structure and function. Refined X-ray structures of the leucine/isoleucine/valine-binding protein and its complex with leucine.

  1989cited by this paper
• Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution.

  1989cited by this paper
• Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution.

  1989cited by this paper
• Structure of the L-leucine-binding protein refined at 2.4 A resolution and comparison with the Leu/Ile/Val-binding protein structure.

  1989cited by this paper
• High‐resolution X‐ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme.

  1989cited by this paper
• Mechanisms of cooperativity and allosteric regulation in proteins

  1989cited by this paper
• Elbow motion in the immunoglobulins involves a molecular ball-and-socket joint

  1988cited by this paper
• Structure‐function relationships in 3‐phosphoglycerate kinase: Role of the carboxy‐terminal peptide

  1988cited by this paper
• Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus.

  1988cited by this paper
• The 2 A resolution structure of the sulfate-binding protein involved in active transport in Salmonella typhimurium.

  1988cited by this paper
• Structure of the complex of adenylate kinase from Escherichia coli with the inhibitor P1,P5-di(adenosine-5'-)pentaphosphate.

  1988cited by this paper
• Flexibility of the DNA‐binding domains of trp repressor

  1988cited by this paper
• Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein.

  1988cited by this paper
• Proteins

  1987cited by this paper
• Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 A resolution.

  1987cited by this paper
• Site-directed mutagenesis of glutamate-190 in the hinge region of yeast 3-phosphoglycerate kinase: implications for the mechanism of domain movement.

  1987cited by this paper
• The crystal structure of trp aporepressor at 1.8 Å shows how binding tryptophan enhances DNA affinity

  1987cited by this paper
• Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin.

  1987cited by this paper
• Transferrins: insights into structure and function from studies on lactoferrin

  1987cited by this paper
• Three-dimensional structure of calmodulin

  1985cited by this paper
• Mechanisms of domain closure in proteins.

  1984cited by this paper
• Human alpha 1-proteinase inhibitor. Crystal structure analysis of two crystal modifications, molecular model and preliminary analysis of the implications for function.

  1984cited by this paper
• Structural and functional aspects of domain motions in proteins.

  1984cited by this paper
• Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 A resolution.

  1984cited by this paper
• Transmission of conformational change in insulin

  1983cited by this paper
• Structural domains in proteins and their role in the dynamics of protein function.

  1983cited by this paper
• Structure of tomato busy stunt virus IV. The virus particle at 2.9 A resolution.

  1983cited by this paper
• Structure of tomato bushy stunt virus IVThe virus particle at 29resolution

  1983cited by this paper
• Location of structural domains in protein.

  1981cited by this paper
• Location of structural domains in proteins

  1981cited by this paper
• Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 A resolution.

  1981cited by this paper

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

  2025cites this paper
• TRAMbio: a flexible python package for graph rigidity analysis of macromolecules

  2025cites this paper
• Enzymes as viscoelastic catalytic machines

  2025cites this paper
• Faster and More Accurate Estimation of Protein Hinges Based on Information Criteria

  2025cites this paper
• Predicting pose distribution of protein domains connected by flexible linkers is an unsolved problem

  2025cites this paper
• Exploring Helical Fraying Linked to Dynamics and Catalysis in Adenylate Kinase

  2025cites this paper
• Transition Path Sampling Guided by Structural Motifs.

  2025cites this paper
• Conformation Heterogeneity of Protein-Ligand Complexes Revealed by Native Mass Spectrometry and Ultraviolet Photodissociation

  2025cites this paper
• CryoEM and crystal structure analyses reveal the indirect role played by Trp89 in glutamate dehydrogenase enzymatic reactions

  2025cites this paper
• Mechanistic and Molecular Dynamics Studies Reveal that Increased Loop 3 Mobility Alters Substrate Capture in an NADH:Quinone Oxidoreductase

  2025cites this paper
• Binding Affinity Determination in Drug Design: Insights from Lock and Key, Induced Fit, Conformational Selection, and Inhibitor Trapping Models

  2024cites this paper
• A low-barrier proton shared between two aspartates acts as a conformational switch that changes the substrate specificity of the β-lactamase BlaC.

  2024cites this paper
• Stimuli-responsive hydrogels based on protein/peptide and their sensing applications

  2024cites this paper
• CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase

  2024cites this paper
• Deep learning of protein energy landscape and conformational dynamics from experimental structures in PDB

  2024cites this paper
• Ligands‐induced open‐close conformational change during DapE catalysis: Insights from molecular dynamics simulations

  2023cites this paper
• Coenzyme‐binding pathway on glutamate dehydrogenase suggested from multiple‐binding sites visualized by cryo‐electron microscopy

  2023cites this paper
• Molecular mechanism study of the structural regulation of the N-terminal domain binding antibody on the receptor binding domain of SARS-CoV-2.

  2023cites this paper
• Dissecting the Structural Dynamics of Authentic Cholesteryl Ester Transfer Protein for the Discovery of Potential Lead Compounds: A Theoretical Study

  2023cites this paper
• Sequence and structure alignments in post-AlphaFold era.

  2023cites this paper
• Revealing Allosteric Mechanism of Amino Acid Binding Proteins from Open to Closed State

  2023cites this paper
• Comparing the Effect of HPP on the Structure and Stability of Soluble and Membrane-Bound Polyphenol Oxidase from ‘Lijiang Snow’ Peach: Multispectroscopic and Molecular Dynamics Simulation

  2023cites this paper
• Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS‐Q

  2023cites this paper
• Specifying conformational heterogeneity of multi-domain proteins at atomic resolution.

  2023cites this paper
• Structural Determinants for Ligand Accommodation in Voltage Sensors

  2022cites this paper
• Positive Selection during Niche Adaptation Results in Large-Scale and Irreversible Rearrangement of Chromosomal Gene Order in Bacteria

  2022influential citation
• Structure determination of high-energy states in a dynamic protein ensemble

  2022cites this paper
• Finite temperature string method with umbrella sampling using path collective variables: application to secondary structure change in a protein.

  2022cites this paper
• A graph-based algorithm for detecting rigid domains in protein structures

  2021cites this paper
• Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1

  2021cites this paper
• Impact of protein conformational diversity on AlphaFold predictions

  2021cites this paper
• Acceleration of enzymatic catalysis by active hydrodynamic fluctuations

  2021cites this paper
• “Protein” no longer means what it used to

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

  2021cites this paper
• Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

  2021cites this paper
• Decline of protein structure rigidity with interatomic distance

  2021cites this paper
• Energy Landscape and Hydration of Proteins

  2021cites this paper
• Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for noncatalytic roles

  2021cites this paper
• Hydration Structure Changes of Proteins at Work

  2021cites this paper
• Dimensional reduction in complex living systems: Where, why, and how

  2021cites this paper
• Time-resolved X-ray scattering studies of proteins.

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

  2021cites this paper
• Structural Analysis of a Genetically Encoded FRET Biosensor by SAXS and MD Simulations

  2021cites this paper
• Linearised loop kinematics to study pathways between conformations

  2021cites this paper
• Probing Conformational Dynamics of Antibodies with Geometric Simulations.

  2021cites this paper
• The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV–vis absorption spectroscopy study

  2021cites this paper
• Transient kinetic studies of the antiviral Drosophila Dicer-2 reveal roles of ATP in self–nonself discrimination

  2021cites this paper
• Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling

  2020cites this paper
• D3PM: a comprehensive database for protein motions ranging from residue to domain

  2020cites this paper
• Comparative dynamics of tropomyosin in vertebrates and invertebrates

  2020cites this paper
• Evolution of Protein Structure and Stability in Global Warming

  2020cites this paper
• Molecular modeling and simulation study of homoserine kinase as an effective leishmanial drug target

  2020cites this paper
• Evidence of Combined Effect of Amino Acid Substitutions within G-H and B-C Loops of VP1 Conferring Serological Heterogeneity in Foot-and-Mouth Disease Virus Serotype A.

  2020cites this paper
• Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins.

  2020cites this paper
• A real-time, transient kinetic study of Drosophila melanogaster Dicer-2 elucidates mechanism of termini-dependent cleavage of dsRNA

  2020cites this paper
• Cytoskeletal Drugs Modulate Off-Target Protein Folding Landscapes Inside Cells.

  2020cites this paper
• The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor

  2020cites this paper
• Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus

  2020cites this paper
• Coarse-grained molecular dynamics simulation of protein conformational change coupled to ligand binding

  2020cites this paper
• Sequence-Based Prediction of Metamorphic Behavior in Proteins

  2020cites this paper
• Overview of Strategies in Fluorescence Sensing

  2020cites this paper
• Molecular Recognition: Lock-and-Key, Induced Fit, and Conformational Selection

  2020cites this paper
• Probabilistic models for protein conformational changes

  2020cites this paper
• Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo‐electron microscopy

  2020cites this paper
• Investigation of sequence features of hinge-bending regions in proteins with domain movements using kernel logistic regression

  2020cites this paper
• Crowder induced structural modulation of a multi-domain protein during its early stages of aggregation: A FRET-based and protein solvation study.

  2019cites this paper
• Shear viscosity of two-state enzyme solutions.

  2019cites this paper
• Crystal structure of citrate synthase (Msed_0281) from Metallosphaera sedula

  2019cites this paper
• Proteins: the physics of amorphous evolving matter

  2019cites this paper
• Structural variations within proteins can be as large as variations observed across their homologues.

  2019cites this paper
• Mechanics of allostery: contrasting the induced fit and population shift scenarios

  2019cites this paper
• Crystal structure of the Fab region of a neutralizing antibody against granulocyte-macrophage colony-stimulating factor.

  2019cites this paper
• Patch-DCA: Improved Protein Interface Prediction by utilizing Structural Information and Clustering DCA scores

  2019cites this paper
• Conferment of CO-Controlled Dimer–Monomer Transition Property to Thermostable Cytochromec′ by Mutation in the Subunit–Subunit Interface

  2019cites this paper
• Crystal structure and biochemical properties of msed_0281, the citrate synthase from Metallosphaera sedula.

  2019cites this paper
• Protein dynamics analysis reveals that missense mutations in cancer‐related genes appear frequently on hinge‐neighboring residues

  2019cites this paper
• Terahertz vibration modes in Na/K-ATPase

  2019cites this paper
• The Open Conformation Satisfies Multiple NMR Experiments on Apo Glutamine-Binding Protein: Overcoming Pitfalls in the Study of Interdomain Dynamics.

  2019cites this paper
• Structure, interactions and self-assembly of ASC-dependent inflammasomes.

  2019cites this paper
• Global response of diacylglycerol kinase towards substrate binding observed by 2D and 3D MAS NMR

  2019cites this paper
• On the dynamical incompleteness of the Protein Data Bank

  2019cites this paper
• A probabilistic network model for structural transitions in biomolecules

  2018cites this paper
• High temperature and pressure influence the interdomain orientation of Nip7 proteins from P. abyssi and P. furiosus: MD simulations

  2018cites this paper
• Phyla-specific Correlated Dynamics in Tropomyosin

  2018cites this paper
• Morphing and docking visualisation of biomolecular structures using Multi-Dimensional Scaling.

  2018cites this paper
• Large scale analysis of protein conformational transitions from aqueous to non-aqueous media

  2018cites this paper
• Exploring Protein Conformational Diversity.

  2018cites this paper
• Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open–Closed Transition

  2018cites this paper
• Raman and Infrared Spectra of Acoustical, Functional Modes of Proteins from All-Atom and Coarse-Grained Normal Mode Analysis

  2018cites this paper
• Structural and Kinetic Studies of Asp632 Mutants and Fully Reduced NADPH-Cytochrome P450 Oxidoreductase Define the Role of Asp632 Loop Dynamics in the Control of NADPH Binding and Hydride Transfer.

  2018cites this paper
• Binding profiles of cholesterol ester transfer protein with current inhibitors: a look at mechanism and drawback

  2018cites this paper
• Application of Graphical Models in Protein-Protein Interactions and Dynamics

  2018cites this paper
• Green function of correlated genes in a minimal mechanical model of protein evolution

  2018cites this paper
• Antigenerkennung durch B-Zell- und T-Zell-Rezeptoren

  2018cites this paper
• Influence of PEGylation on Domain Dynamics of Phosphoglycerate Kinase: PEG Acts Like Entropic Spring for the Protein.

  2018cites this paper
• Native state protein dynamics

  2018cites this paper
• Development and evaluation of protein quantitation assays for use in health care

  2018cites this paper
• Allosteric modulation of pentameric ligand-gated ion channels by general anesthetics

  2018cites this paper
• Conformational diversity analysis reveals three functional mechanisms in proteins

  2017cites this paper
• High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments.

  2017cites this paper