Biomaterial Database

Molecular dynamics simulation of Pf1 coat protein. 1993

D J Tobias, and M L Klein, and S J Opella

Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323.

The results of molecular dynamics simulations of Pf1 coat protein are described and compared to experimental NMR data on both the membrane bound and structural forms of this viral coat protein. Molecular dynamics simulations of the 46 residue coat protein and related model sequences were performed according to a simple protocol. The simulations were initiated with the polypeptides in a completely uniform alpha helical conformation in a dielectric continuum (epsilon = 2) and the motions of individual residues were followed as a function of time by monitoring the angular fluctuations of amide NH bond vectors. The simulations of Pf1 coat protein were able to identify the same mobile and structured segments found in experimental NMR studies of the membrane bound form of the protein (Shon, K.-J., Y. Kim, L. A. Colnago, and S. J. Opella. 1991. Science (Wash. DC). 252:1303-1305). Significantly, in addition to mobile amino and carboxyl terminal regions, a mobile internal loop was found that connects the rigid hydrophobic and amphipathic helices in the protein. NMR experiments show that this mobile loop is present in both the viral and membrane bound forms of the protein and that it plays a role in viral assembly (Nambudripad, R., W. Stark, S. J. Opella, and L. Makowski. 1991. Science (Wash. DC) 252:1305-1308). The results of simulations of several alanine based 46 residue polypeptides with some of the charged residues present in the Pf1 coat protein sequence suggest that interactions between the Asp 14 and Asp 18 sidechains and the peptide backbone are responsible for the formation of the mobile loop. The agreement between the results of the calculations presented here and the previously reported NMR experiments suggest that molecular dynamics simulations might be useful in the prediction of the secondary structure and dynamics of individual residues in membrane and structural proteins with predominantly alpha helical secondary structure.

UI	MeSH Term	Description	Entries
D008956	Models, Chemical	Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.	Chemical Models,Chemical Model,Model, Chemical
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D009682	Magnetic Resonance Spectroscopy	Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).	In Vivo NMR Spectroscopy,MR Spectroscopy,Magnetic Resonance,NMR Spectroscopy,NMR Spectroscopy, In Vivo,Nuclear Magnetic Resonance,Spectroscopy, Magnetic Resonance,Spectroscopy, NMR,Spectroscopy, Nuclear Magnetic Resonance,Magnetic Resonance Spectroscopies,Magnetic Resonance, Nuclear,NMR Spectroscopies,Resonance Spectroscopy, Magnetic,Resonance, Magnetic,Resonance, Nuclear Magnetic,Spectroscopies, NMR,Spectroscopy, MR
D002213	Capsid	The outer protein protective shell of a virus, which protects the viral nucleic acid. Capsids are composed of repeating units (capsomers or capsomeres) of CAPSID PROTEINS which when assembled together form either an icosahedral or helical shape.	Procapsid,Prohead,Capsids,Procapsids,Proheads
D003198	Computer Simulation	Computer-based representation of physical systems and phenomena such as chemical processes.	Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D001435	Bacteriophages	Viruses whose hosts are bacterial cells.	Phages,Bacteriophage,Phage
D001703	Biophysics	The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.	Mechanobiology
D017433	Protein Structure, Secondary	The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to ALPHA-HELICES; BETA-STRANDS (which align to form BETA-SHEETS), or other types of coils. This is the first folding level of protein conformation.	Secondary Protein Structure,Protein Structures, Secondary,Secondary Protein Structures,Structure, Secondary Protein,Structures, Secondary Protein
D055592	Biophysical Phenomena	The physical characteristics and processes of biological systems.	Biophysical Concepts,Biophysical Processes,Biophysical Phenomenon,Biophysical Process,Biophysical Concept,Concept, Biophysical,Concepts, Biophysical,Phenomena, Biophysical,Phenomenon, Biophysical,Process, Biophysical,Processes, Biophysical
D036022	Capsid Proteins	Proteins that form the CAPSID of VIRUSES.	Procapsid Protein,Procapsid Proteins,Viral Coat Protein,Viral Coat Proteins,Viral V Antigens,Viral V Proteins,Capsid Protein,Viral Outer Coat Protein,Antigens, Viral V,Coat Protein, Viral,V Antigens, Viral,V Proteins, Viral