May 5, 1989

Dynamical structure of carboxypeptidase A

Journal of Molecular Biology
M W MakinenW F van Gunsteren

Abstract

Structural fluctuations of the apoenzyme form of carboxypeptidase A (EC 3.4.12.2) have been evaluated on the basis of molecular dynamics. The Konnert-Hendrickson refined coordinates of 2437 non-hydrogen atoms of the 307 amino acid residues derived from the X-ray structure of the holoenzyme served as the molecular model together with 548 calculated polar hydrogen atoms and 25 buried solvent molecules. Molecular dynamics simulations were carried out at 277 K, and the averaged structural properties of the protein were evaluated for the terminal 20 picosecond portion of a 48 picosecond trajectory. The average atomic displacement from the initial X-ray structure was 2.49 A for all atoms and 1.79 A for C alpha atoms. The average root-mean-square (r.m.s.) fluctuation of all atoms was 0.67 A as compared to 0.54 A evaluated from the X-ray-defined temperature factors. Corresponding r.m.s. fluctuations for backbone atoms were 0.56 A by molecular dynamics and 0.49 A by X-ray. On the basis of these molecular dynamics studies of the isolated molecule, it is shown that amino acid residues corresponding to intermolecular contact sites of the crystalline enzyme are associated with high amplitude motion. All eight segments of alpha-helix and eig...Continue Reading

  • References11
  • Citations14

References

  • References11
  • Citations14

Citations

Mentioned in this Paper

Molecular Dynamics
CPA1
Carboxypeptidase A
Fluctuation
Carboxypeptidase A5
Molecular Helix
Apoenzymes
Carboxy-Terminal Amino Acid
Plain X-ray
Helix (Snails)

About this Paper

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Coronavirus Protein Structures

Deciphering and comparing the proteins of different coronaviruses forms a basis for understanding SARS-CoV-2 evolution and virus-receptor interactions. This feed follows studies analyzing the structures of coronavirus proteins, thereby revealing potential drug target sites.

DDX3X Syndrome

DDX3X syndrome is caused by a spontaneous mutation at conception that primarily affects girls due to its location on the X-chromosome. DDX3X syndrome has been linked to intellectual disabilities, seizures, autism, low muscle tone, brain abnormalities, and slower physical developments. Here is the latest research.

ALS: Stress Granules

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease characterized by cytoplasmic protein aggregates within motor neurons. TDP-43 is an ALS-linked protein that is known to regulate splicing and storage of specific mRNAs into stress granules, which have been implicated in formation of ALS protein aggregates. Here is the latest research.

Fusion Oncoproteins in Childhood Cancers

This feed explores the function of fusion oncoproteins in specific childhood cancers, including those from racial/ethnic minority and underserved groups, and to provide preclinical assessment of potential therapeutics and how fusion oncoproteins influence gene expression to perturb normal cellular programs to block lineage differentiation and development

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.

Mitotic-exit networks with cytokinesis

Cytokinesis is the highly regulated process that physically separates daughter and mother cells in late mitosis. The mitotic-exit network (MEN), the signalling pathway that drives mitotic exit, directly regulates cytokinesis. Discover the latest research on mitotic-exit networks with cytokinesis here.

DNA Replication Origin

DNA replication is initiated as specific gene sequences, called origins, that function to start DNA replication. Pre-replication complexes are assembled at these origins during the G1 phase of the cell cycle. These sequences allow for targeted activation or deactivation of replication. Discover the latest research on DNA replication origins here.