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Study of how proteins move and change shape
phenomena such as allosteric signaling and enzyme catalysis. The study of protein dynamics is most directly concerned with the transitions between these states
Protein_dynamics
Three-dimensional arrangement of atoms in an amino acid-chain molecule
DJ (2011). "Proteins MOVE! Protein dynamics and long-range allostery in cell signaling". Protein Structure and Diseases. Advances in Protein Chemistry and
Protein_structure
Change of a linear protein chain to a 3D structure
function, although some parts of functional proteins may remain unfolded, indicating that protein dynamics are important. Failure to fold into a native
Protein_folding
Class of molecular proteins
and possesses piezoelectric properties. ATP synthase Cytoskeleton Protein dynamics Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts
Motor_protein
Protein without a fixed 3D structure
freely twist and rotate to recruit their binding partners via protein domain dynamics. They also allow their binding partners to induce larger scale
Intrinsically disordered proteins
Intrinsically_disordered_proteins
Biomolecule consisting of chains of amino acid residues
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions
Protein
Computer simulations to discover and understand chemical properties
(August 2012). "Refinement of protein structure homology models via long, all-atom molecular dynamics simulations". Proteins. 80 (8): 2071–2079. doi:10.1002/prot
Molecular_dynamics
Proteins that are part of, or interact with, biological membranes
Membrane proteins are common proteins that are part of, or interact with, biological membranes. Membrane proteins fall into several broad categories depending
Membrane_protein
German-American physicist
his research has been focused on protein structure, dynamics and stability, and on the relation of these to protein function. He is a structural biologist
Gerhard_Wagner_(physicist)
Powered mechanical device
DJ (2011). "Proteins MOVE! Protein dynamics and long-range allostery in cell signaling". Protein Structure and Diseases. Advances in Protein Chemistry and
Machine
Interdisciplinary science
are often used to visualize structures of biological significance. Protein dynamics can be observed by neutron spin echo spectroscopy. Conformational changes
Biophysics
plane flips in the dynamics of the native state has been inferred in some proteins by comparing crystal structures of the same protein in multiple conformations
Peptide_plane_flipping
Class of enzymes
differs based on their target proteins and location. Various approaches have been applied to study the structure, dynamics and functioning of chaperones
Chaperone_(protein)
Biological molecules for computations
Biological computers use biologically derived molecules — such as DNA and/or proteins — to perform digital or real computations. The development of biocomputers
Biological_computing
Swedish biochemist (born 1959)
and 2023, he served as chair of the Nobel Committee for Chemistry. "Protein dynamics and interactions". Food and Agriculture Organization of the United
Johan_Åqvist
Neutron scattering technique
internal protein dynamics in the proteins NHERF1 and Taq polymerase and the adherens junction, allowing the direct visualization of protein nanomachinery
Neutron_spin_echo
Regulation of enzyme activity
bind to the protein, often resulting in a conformational change and/or a change in protein dynamics. Effectors that enhance the protein's activity are
Allosteric_regulation
Biological molecular machines
Molecular machines Molecular mechanics Molecular propeller Motor proteins Nanomotor Protein dynamics Synthetic molecular motors Bustamante C, Chemla YR, Forde
Molecular_motor
Artificial intelligence program by DeepMind
perfect answer to the protein prediction problem still leaves questions about the protein folding problem (and thus protein dynamics)—understanding in detail
AlphaFold
Interdisciplinary research area
are often used to visualize structures of biological significance. Protein dynamics can be observed by neutron spin echo spectroscopy. Conformational changes
Molecular_biophysics
Man-made molecular machines
has traditionally referred to a naturally occurring protein that induces motion (via protein dynamics), some groups also use the term when referring to
Synthetic_molecular_motor
Spectroscopic technique
involving single crystal sucrose, fructose, oxalic acid, and molecular protein crystals in which the spatial orientation of molecular vibrations are of
Anisotropic terahertz microspectroscopy
Anisotropic_terahertz_microspectroscopy
American scientist
but has recently focused on applying his knowledge to the study of protein dynamics. In 2003, Thorpe joined Arizona State University from Michigan State
Michael_Thorpe
Catalysis of chemical reactions by enzymes
e. lock and key catalysis), as well as motional effects involving protein dynamics Mechanisms of enzyme catalysis vary, but are all similar in principle
Enzyme_catalysis
Category of proteins
Intrinsically disordered proteins Protein dynamics Perdigão, Nelson; Rosa, Agostinho (2019). "Dark Proteome Database: Studies on Dark Proteins". High-Throughput
Dark_proteome
Protein family
well as their protein dynamics, are highly conserved over hundreds of millions of years in tissue forming life forms. Bcl-2 family proteins have a general
Bcl-2_family
mechanical aspects of its long-time large-scale dynamics. The model has a wide range of applications from small proteins such as enzymes composed of a single domain
Gaussian_network_model
Internationally financed scientific facility
allows investigations into macromolecular assemblies, particularly protein dynamics and biomolecular structure. It is a world-renowned centre for nanoscale
Institut_Laue–Langevin
Protein-coding gene in the species Homo sapiens
Mitochondrial dynamics protein MID49 is a protein that in humans is encoded by the MIEF2 gene (from "Mitochondrial elongation factor 2"). Alternative
Mitochondrial dynamics protein MID49
Mitochondrial_dynamics_protein_MID49
Type of antibody
the binding site may play an important role, in particular through protein dynamics. Some abzymes have been engineered to use metal ions and other cofactors
Abzyme
Italian-American biophysicist
Weber at the University of Illinois at Urbana-Champaign, studying protein dynamics. In 1978 he was appointed assistant professor in the Department of
Enrico_Gratton
Type of stable macromolecular complex
polypeptide chain. Protein complexes are a form of quaternary structure. Proteins in a protein complex are linked by non-covalent protein–protein interactions
Protein_complex
Concept on molecular modeling
"CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic
Force_field_(chemistry)
Macromolecular machine that synthesizes proteins in cells
dynamics of eEF2 during GTP hydrolysis. Ribosomes are minute particles consisting of RNA and associated proteins that function to synthesize proteins
Ribosome
How drugs induce reversible suppression of consciousness
Canlas CG, Cui T, Li L, Xu Y, Tang P (2008). "Anesthetic modulation of protein dynamics: insights from a NMR study". Journal of Physical Chemistry B. 112 (45):
Theories of general anaesthetic action
Theories_of_general_anaesthetic_action
Process of introducing a phosphate group on to a protein
hydrophobic portion of a protein into a polar and extremely hydrophilic portion of a molecule. In this way protein dynamics can induce a conformational
Protein_phosphorylation
Chemical compound
synthesis of ligands for metal complexation in EPR/NMR, and probing protein dynamics during folding or catalysis. It is incorporated using orthogonal tRNA/synthetase
Azidophenylalanine
Field of structural biology
spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes. The field was pioneered
Nuclear magnetic resonance spectroscopy of proteins
Nuclear_magnetic_resonance_spectroscopy_of_proteins
The Membrane Protein Structural Dynamics Consortium (MPSDC) is a large scale collaborative consortium composed of an interdisciplinary team of scientists
Membrane Protein Structural Dynamics Consortium
Membrane_Protein_Structural_Dynamics_Consortium
American biochemist, researcher, and academic
on protein structure, protein dynamics, and computational biology, with a specific emphasis on understanding the correlation between the dynamics of proteins
George_N._Phillips
Molecular dynamics software
kernel. Core22, also developed at the Pande lab, uses OpenMM to perform protein dynamics simulations on GPUs via CUDA and OpenCL. During the COVID-19 pandemic
OpenMM
Raman spectroscopy technique
to examine the dynamics of excited electronic states, binding of oxygen or other gases to heme-containing proteins, and protein dynamics. Resonance hyper-Raman
Resonance_Raman_spectroscopy
Distributed computing project simulating protein folding
diseases by the means of simulating protein dynamics. This includes the process of protein folding and the movements of proteins, and is reliant on simulations
Folding@home
Type of biological prediction
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of
Protein_structure_prediction
Inhibitors of translation
A protein synthesis inhibitor is a compound that stops or slows the growth or proliferation of cells by disrupting the processes that lead directly to
Protein_synthesis_inhibitor
Database of protein conformations
The conformational dynamics data bank (CDDB) is a database about conformational dynamics of heavy proteins and protein assemblies. The CDDB is useful
Conformational dynamics data bank
Conformational_dynamics_data_bank
Matter which can change its physical properties in a programmable fashion
specific functions, such as substrate adhesion, nanoparticle templating, and protein immobilization. Science portal Technology portal Computronium Nanotechnology
Programmable_matter
Field of Study
metal ion. The structures of many large protein assemblies, such as ATP synthase, also exhibit machine-like dynamics as they act on their substrates. Similarly
Biophysical_chemistry
Italian physicist and historian of science
Chicago". "The Emergence of Protein Dynamics Simulations". Springer Link. "SHAKE and the Exact Constraint Satisfaction of the Dynamics of Semi-Rigid Molecules"
Daniele_Macuglia
used to determine protein structures, protein folding, protein dynamics, and protein–protein interactions. Unlike nucleic acids, proteins oxidize rather
Protein_footprinting
Protein complexes at cell junctions
plakoglobin and links the actin cytoskeleton with cadherin. Significant protein dynamics are thought to be involved. Adherens junctions were, for many years
Adherens_junction
Study of the mechanics of biological systems
level, from whole organisms to organs, cells and cell organelles, and even proteins. Biomechanics is a branch of biophysics. The word "biomechanics" (1899)
Biomechanics
Glycoprotein spike on a viral capsid or viral envelope
called spike protein, formerly known as E2) is the largest of the four major structural proteins found in coronaviruses. The spike protein assembles into
Coronavirus_spike_protein
such as metal deposition, dynamics of thin water films and diffusion processes, biomineralization processes, protein dynamics and structure, single-molecule
Liquid-Phase Electron Microscopy
Liquid-Phase_Electron_Microscopy
American chemist
Ahn investigates the internal motions of protein kinases, specifically studying their coupling protein dynamics and catalytic function. Ahn studies the
Natalie_Ahn
British molecular biologist
discovered experimentally-validated lead compounds for many different protein targets and for a variety of diseases such as diabetes, prostate cancer
Jeremy_C._Smith
having a distinctive DNA sequence. Examples include macromolecules such as proteins and nucleic acids, biomolecular complexes such as a ribosome, and structures
Cellular_component
P38 mitogen-activated protein kinases
enzymes of the STE protein kinase group. In this way protein dynamics can induce a conformational change in the structure of the protein via long-range allostery
Mitogen-activated protein kinase
Mitogen-activated_protein_kinase
Bioinformatics subfield
prediction of protein structure and folding, thermodynamic stability, protein-protein and protein-ligand interactions, docking and molecular dynamics analyses
Structural_bioinformatics
proteins move along microtubule strands in muscle cells. Single-molecule imaging in live cells reveals interesting information about protein dynamics
Single-molecule_experiment
Classification of ions for denaturating proteins
Peters, Judith; Dér, András (October 2013). "Hofmeister ions control protein dynamics". Biochimica et Biophysica Acta (BBA) - General Subjects. 1830 (10):
Hofmeister_series
Induced shape change in macromolecules
changes can be visualized.[citation needed] Database of protein conformational diversity Protein dynamics The Database of Macromolecular Motions (molmovdb)
Conformational_change
System of communication
JAK-STAT signaling pathway Imd pathway Localisation signal Oscillation Protein dynamics Systems biology Lipid signaling Redox signaling Signaling cascade Cell
Cell_signaling
Scientific discipline
to assess a number of protein dynamics including protein tracking, conformational changes, protein–protein interactions, protein synthesis and turnover
Chemical_biology
Turkish biochemist
biopolymers, computational structural biology, protein dynamics, binding and folding of proteins, and protein interactions. She is a professor in the department
Türkan_Haliloğlu
Hospital A, Gelpi JL, Orozco M (2007-01-16). "A consensus view of protein dynamics". PNAS. 104 (3): 796–801. Bibcode:2007PNAS..104..796R. doi:10.1073/pnas
Lindemann_index
Ability to move using metabolic energy
This depicts translation - a motile nanoscale molecular process using protein dynamics. Cell migration Metaboly Clegg, Chris (2008). "3.2 Cells make organisms"
Motility
Application of mass spectrometry
Protein mass spectrometry refers to the application of mass spectrometry to the study of proteins. Mass spectrometry is an important method for the accurate
Protein_mass_spectrometry
Protein structure at the base of cilia or flagella
H.; Winey, M. (2009). "Basal body components exhibit differential protein dynamics during nascent basal body assembly". Molecular Biology of the Cell
Basal_body
Branch of chemistry
In addition, supramolecular systems have been designed to disrupt protein–protein interactions that are important to cellular function. Supramolecular
Supramolecular_chemistry
Biological concepts and questions with insufficient resolutions
design methods still skip over how proteins end up in the final shape (folding mechanism and kinetics; protein dynamics). Wet lab methods of the 2020s allow
List of unsolved problems in biology
List_of_unsolved_problems_in_biology
Self-stable region of a protein's chain that folds independently from the rest
protein vibrational dynamics: comparing molecular dynamics and gaussian models, Proteins, 55, 635, 2004. Barclay AN (August 2003). "Membrane proteins
Protein_domain
Indian biophysicist and biochemist
of Technology Madras. He is known for his studies in the fields of protein dynamics, green chemistry and nanoclusters and is a Fulbright scholar. The Department
Sanjib_Senapati
Organelle found on eukaryotic cells
device Protein dynamics#Global flexibility: multiple domains – Study of how proteins move and change shape Protein domain#Domains and protein flexibility –
Cilium
Measurand in NMR spectroscopy
simple model of slow dynamics to remedy this. However, for many classes of proteins, including intrinsically disordered proteins, analysis of RDCs becomes
Residual_dipolar_coupling
Protein-coding gene in the species Homo sapiens
involving significant protein dynamics. Members of the ezrin (VIL2; MIM 123900)-radixin (RDX; MIM 179410)-moesin (MSN; MIM 309845) (ERM) protein family are highly
Sodium-hydrogen antiporter 3 regulator 1
Sodium-hydrogen_antiporter_3_regulator_1
Biochemical analysis procedure
The structural dynamics response (SDR) assay is a type of biophysical test used to measure ligand binding to a target protein. The assay is configured
Structural Dynamics Response Assay
Structural_Dynamics_Response_Assay
Grouping of proteins
structural motifs are highly conserved. Some protein dynamics and conformational changes of the protein structure may also be conserved, as is seen in
Protein_superfamily
German]; Marcus, R. A. (2002). "On the relation of protein dynamics and exciton relaxation in pigment–protein complexes: An estimation of the spectral density
Fenna–Matthews–Olson_complex
Straight path on a curved surface or a Riemannian manifold
(intermediates) and saddle points (transition states). In molecular dynamics, protein conformations can be treated as points on a curved manifold, wherein
Geodesic
Protein found in humans
Alpha-synuclein (aSyn) is a protein that in humans is encoded by the SNCA gene. It is a neuronal protein involved in the regulation of synaptic vesicle
Alpha-synuclein
Protocol in biochemistry
NMR and molecular dynamics ensembles from this parameter. The key advantages of this protocol over existing methods of studying protein flexibility are
Random_coil_index
Protein family
Compendium of protein lysine acetylation Enzyme assay Organic synthesis Protein dynamics Proteolysis The Proteolysis Map Bürger M, Willige BC, Chory J (December
SOBER1
Lab technique in molecular biology
stop protein synthesis or radioisotopic amino acids or proteins such as green fluorescent protein (GFP). These labels are used to study proteins through
Pulse-chase_analysis
American biophysicist
Black, Ben E.; Englander, S. Walter (2012-06-11). "Protein dynamics viewed by hydrogen exchange". Protein Science. 21 (7): 996–1005. doi:10.1002/pro.2081
S._Walter_Englander
Protein-coding gene in humans
molecular on/off switch, using protein dynamics. Once it is allosterically activated, it recruits and activates proteins necessary for the propagation
KRAS
Movement of entangled polymer chains
dynamics of shorter chains or of long chains at short times is usually described by the Rouse model. Polymer characterization Polymer physics Protein
Reptation
differential expression of a protein marker level in a single experiment. It is also used for monitoring protein dynamics in response to various stimuli
Reverse phase protein lysate microarray
Reverse_phase_protein_lysate_microarray
Molecular device capable of converting energy into movement
motor protein would be able to move a "cargo" within that device, via protein dynamics, similarly to how kinesin moves various molecules along tracks of microtubules
Nanomotor
System for validating protein structures
spectroscopy Protein nuclear magnetic resonance spectroscopy Protein dynamics#Domains and protein flexibility Random Coil Index GeNMR Protein structure prediction
Protein Structure Evaluation Suite & Server
Protein_Structure_Evaluation_Suite_&_Server
American physician (born 1943)
Anderson, RW; DeVries, WC (April 1976). "Transvascular fluid and protein dynamics in the lung following hemorrhagic shock". J. Surg. Res. 20: 281–90
William_DeVries
Polymer of tubulin that forms part of the cytoskeleton
and other proteins important for regulating microtubule dynamics. Recently an actin-like protein has been found in the gram-positive bacterium Bacillus
Microtubule
European magnetic resonance society
Lindale: Understanding and Optimizing Dynamics in Hyperpolarized Magnetic Resonance 2021: Reid Alderson: Protein folding investigated by NMR spectroscopy
Groupement_Ampère
Protein complex that allows microtubules to attach to chromosomes during cell division
Kinetochore proteins and proteins binding to MTs (+) end (collectively called +TIPs) regulate kinetochore movement through the kMTs (+) end dynamics regulation
Kinetochore
Carlo MD – Molecular dynamics Min – Optimization QM – Quantum mechanics REM – Replica exchange method Car–Parrinello molecular dynamics Comparison of force-field
Comparison of software for molecular mechanics modeling
Comparison_of_software_for_molecular_mechanics_modeling
American chemist and academic
Society Council Linda Columbus; Wayne L Hubbell (2002). "A new spin on protein dynamics". Trends in Biochemical Sciences. 27 (6): 288–295. doi:10.1016/s0968-0004(02)02095-9
Linda_Columbus
biophysics of individual molecules (e.g. measurements of protein dynamics and DNA and RNA dynamics, activity of ion channels, enzyme activity, quantum dots
Reduced_dimensions_form
lipids adjacent to the protein? 2) Do membrane proteins have long-range effects on the order or dynamics of membrane lipids? 3) How do the lipids influence
Protein–lipid_interaction
biophysics of individual molecules (e.g. measurements of protein dynamics and DNA and RNA dynamics, activity of ion channels, enzyme activity, quantum dots)
Two-state_trajectory
Theory describing chemical reaction rates
Surfaces. New York: Wiley. Pineda, J. R.; Schwartz, S. D. (2006). "Protein dynamics and catalysis: The problems of transition state theory and the subtlety
Transition_state_theory
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