Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation.

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. Abstract Text:

Hongxing Lei,Yong Duan,

Ab initio folding with all-atom model remains to be a difficult task even for small proteins. In this report, we conducted an accumulated 24 mus simulations on the wild type and two mutants of albumin binding domain (ABD) using the AMBER FF03 all-atom force field and a generalized-Born solvation model. Folding events have been observed in multiple trajectories, and the best folded structures achieved root-mean-square deviation (RMSD) of 2.0 A. The folding of this three-helix bundle protein followed a diffusion-collision process, where substantial formation of the individual helices was critical and preceded the global packing. Owing to the difference in the intrinsic helicity, helix I formed faster than the other two helices. The order of the formation of helices II and III varied in different trajectories, indicating heterogeneity of the folding process. The slightly shifted boundaries of the helical segments had direct impact on the global packing, suggesting room for improvement on the simulation force field and solvation model.

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. Publishing Authors By Initials

H Lei,Y Duan,

For similar biochemical phenomena, metabolism, and nutrition: biochemical phenomena: molecular structure: molecular conformation: protein conformation: protein structure, tertiary research abstracts see: biochemical phenomena, metabolism, and nutrition: biochemical phenomena: molecular structure: molecular conformation: protein conformation: protein structure, tertiary research

PUBMED ID PMID:

MEDLINE DATE:

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: The journal of physical chemistry. B

VOLUME: 111

Page Numbers: 5458-63

Journal Abbreviation:

ISSN: 1520-6106

DAY: 26

MONTH: 04

YEAR: 2007

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 101157530

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. Keywords Mesh Terms:

KEYWORDS: Protein Structure, Tertiary

MESH TERMS: chemistry

Chemical & Substance for Abstract: Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. Information

Substance Name: Albumins

Registry Number: 0

Grant and Affiliation Information for Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation.

AFFILIATION: Genome Center and Department of Applied Science, One Shields Avenue, Davis, California 95616, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM67168

ACRONYM: GM

MEDLINETA: J Phys Chem B

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation Related Publications

• An Automatic and Power Spectra-based Rotate Correcting Algorithm for Microarray Image.
• Challenges and opportunities in dystrophin-deficient cardiomyopathy gene therapy.
• Chiral selective effects of doxazosin enantiomers on blood pressure and urinary bladder pressure in anesthetized rats.
• Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein A.
• Diffuse Alveolar Lesion in BALB/c Mice Induced with Human Reovirus BYD1 Strain and its Potential Relation with SARS.
• Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulations.
• From the smallest virus to the biggest gene: marching towards gene therapy for duchenne muscular dystrophy.
• In vitro and in vivo evaluation of a novel oral insulin formulation.
• Phenol red interacts with the protofibril-like oligomers of an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contacts.
• Synthetic intron improves transduction efficiency of trans-splicing adeno-associated viral vectors.
• [A research on healthcare integrating model of medical information system]
• [Application of functional magnetic resonance imaging (fMRI) in the study of visceral hypersensitivity of the gut]
• [Calcium-dependent chloride channels in plasma membrane of oocytes from toad, Bufo bufo gargarizans]
• [Clinical profiles of circulating dendritic cell phenotype and lymphocyte subsets in patients chronically infected with HBV during lamivudine treatment]
• [Clinical value of monitoring CD14+ monocyte human leukocyte antigen (locus) DR levels in the early stage of sepsis]
• [Determination of copper and chromium in the cartridges of permanent marker pen and ink by ICP-AES]
• [Development of an immunochromayography assay method for the detection of Yersinia pestis]
• [Early prenatal diagnosis using fetal cells acquired from different sites of uterine cervix: a preliminary study]
• [Electrocardiograph beat pattern recognition]
• [Expression of CD44 and nm23-H1 protein in the primary and metastatic lymph node lesions in supraglottic and hypopharyngeal cancer]
• [Increasing the speed of construction of the public health incident command system in our country]
• [Induction of growth-associated protein-43 expression in airway afferent nerves of guinea pigs by allergic airway inflammation]
• [Influence of anisodamine on heat-stress in rats]
• [Interatomic distances of molecule for orthohydrogen and parahydrogen]
• [Isolation and identification of Bacillus anthracis in an accidental case]
• [Isolation and identification of Streptococcus suis serotype 2 from sick-pig samples of Sichuan province]
• [Study of sensitivity to impulse noise in guinea pig, rat and mouse]
• [Study on aqueous extraction process for preparation of yuxianling granules]
• [Three types of induced bursting rhythm in rat injured nerves]
• [Zhang Taiyan's Academic Position and Achievements in the Modern History of Chinese Medicine.]