Search research articles

Search research articles

Related Experiment Videos

Characterization of "native" apomyoglobin by molecular dynamics simulation.

¹Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213.

Journal of Molecular Biology

|September 20, 1992

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

A novel agent SL-401 induces anti-myeloma activity by targeting plasmacytoid dendritic cells, osteoclastogenesis and cancer stem-like cells.

Leukemia·2017

Same author

Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes.

The journal of physical chemistry letters·2012

Same author

Inactivation of HAUSP in vivo modulates p53 function.

Oncogene·2009

Same author

CHARMM: the biomolecular simulation program.

Journal of computational chemistry·2009

Same author

The p53--Mdm2--HAUSP complex is involved in p53 stabilization by HAUSP.

Oncogene·2007

Same author

ARF-BP1 as a potential therapeutic target.

British journal of cancer·2006

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Molecular dynamics simulations reveal distinct flexible and rigid regions in apomyoglobin. These findings support the theory that specific helical subdomains remain stable during protein unfolding.

Area of Science:

Protein dynamics and structural biology
Computational biophysics
Biochemistry

Background:

Protein folding intermediates are crucial for understanding protein structure and function.
Pulsed H/2H exchange experiments by Hughson et al. provided insights into apomyoglobin structure and motion.
Apomyoglobin's structural changes during unfolding are not fully understood.

Purpose of the Study:

To investigate the structure and dynamics of native apomyoglobin using molecular dynamics simulations.
To complement experimental studies on protein folding intermediates.
To identify conformationally labile and non-labile regions in apomyoglobin.

Main Methods:

Molecular dynamics simulations of native apomyoglobin in aqueous solution.

Related Experiment Videos

Analysis of protein structure and fluctuations over 0.5 nanoseconds.

Comparison of simulation results with experimental data (pulsed H/2H exchange, NMR, crystallographic B-factors).

Main Results:

Local fluctuations in apomyoglobin simulations align with experimental data for both apo- and holoprotein.
Conformationally labile regions (helices C, D, F) and non-labile regions (helices A, B, E, G, H) were identified.
Shifting motions of helices C, D, and F into the vacant heme cavity were observed as a key difference between holo- and apomyoglobin.

Conclusions:

The simulation model for apomyoglobin structure and fluctuations complements experimental findings.
Helices A, G, and H form a rigid subdomain that likely remains native-like during pH-induced unfolding.
The identified labile and stable regions support the concept of distinct folding subdomains in protein unfolding.