Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

A molecular dynamics analysis of protein structural elements.

C B Post1, C M Dobson, M Karplus

  • 1Chemistry Department, Purdue University, West Lafayette, Indiana 47907.

Proteins
|January 1, 1989
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Structural Characteristics of α-Synuclein Oligomers.

International review of cell and molecular biology·2017
Same author

Spatial propagation of protein polymerization.

Physical review letters·2014
Same author

The effects of guanidine hydrochloride on the 'random coil' conformations and NMR chemical shifts of the peptide series GGXGG.

Journal of biomolecular NMR·2010
Same author

Amyloidogenicity and aggregate cytotoxicity of human glucagon-like peptide-1 (hGLP-1).

Protein and peptide letters·2009
Same author

Disseminated gonococcal infection in pregnancy.

Journal of obstetrics and gynaecology : the journal of the Institute of Obstetrics and Gynaecology·2009
Same author

CHARMM: the biomolecular simulation program.

Journal of computational chemistry·2009
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

Protein structure influences internal motions, with rigid elements showing less fluctuation than flexible loops. Substrate binding alters these dynamics, affecting specific loop and helix movements in hen egg-white lysozyme.

Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Protein dynamics are crucial for function.
  • Understanding the relationship between protein structure and motion is key to deciphering biological mechanisms.

Purpose of the Study:

  • To investigate the correlation between protein secondary structure and internal dynamics.
  • To analyze how substrate binding affects protein motion in hen egg-white lysozyme.

Main Methods:

  • Utilized molecular dynamics simulations.
  • Calculated positional fluctuations of secondary structure elements (helices, beta-sheets, loops).
  • Compared dynamics in free and substrate-bound states of hen egg-white lysozyme.

Main Results:

Related Experiment Videos

  • Helices and beta-sheets exhibited lower, converged fluctuations, while loops showed higher, un-converged fluctuations.
  • Substrate binding reduced motion in an active site loop (residues 101-107).
  • A loop and 3(10) helix (residues 67-88) not interacting with the substrate displayed increased fluctuations; helix reorientation occurred over 55 ps.

Conclusions:

  • Protein secondary structure dictates distinct internal motion patterns.
  • Substrate binding dynamically modulates protein flexibility, impacting specific regions.
  • Observed changes in dynamics are not due to sampling errors but reflect allosteric effects or conformational adjustments.