Biomaterial Database

Probing the Conformational Dynamics of the Bioactive Peptide TLQP-21 in Solution: A Molecular Dynamics Study. 2015

Sandipan Chakraborty, and Shamim Akhter, and Jesús R Requena, and Soumalee Basu

Department of Microbiology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700 019, India.

VGF-derived peptide, TLQP-21, is a physiologically active neuropeptide exhibiting important roles in energy expenditure and balance, gastric contractility, reproduction, pain modulation, and stress. Although the physiological functions of the peptide constitute a research area of considerable interest, structural information is clearly lacking. Here, using extensive 550 nanoseconds molecular dynamics simulation in explicit water model, we have explored the folding energy landscape of the peptide. Principal component analysis and cluster analysis have been used to identify highly populated conformational states of the peptide in solution. The most populated structure of the peptide adopts a highly compact globular form stabilized by several hydrogen-bonding interactions and π-cationic interactions. Strong surface complementarity of hydrophobic residues allows tighter spatial fit of the residues within the core region of the peptide. Our simulation also predicts that the peptide is highly flexible in solution and that the region A7 -R9 and three C-terminal residues, P19 -R21 , possess strong helical propensity.

UI	MeSH Term	Description	Entries
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D010446	Peptide Fragments	Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.	Peptide Fragment,Fragment, Peptide,Fragments, Peptide
D000595	Amino Acid Sequence	The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.	Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
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
D017510	Protein Folding	Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.	Protein Folding, Globular,Folding, Globular Protein,Folding, Protein,Foldings, Globular Protein,Foldings, Protein,Globular Protein Folding,Globular Protein Foldings,Protein Foldings,Protein Foldings, Globular
D056004	Molecular Dynamics Simulation	A computer simulation developed to study the motion of molecules over a period of time.	Molecular Dynamics Simulations,Molecular Dynamics,Dynamic, Molecular,Dynamics Simulation, Molecular,Dynamics Simulations, Molecular,Dynamics, Molecular,Molecular Dynamic,Simulation, Molecular Dynamics,Simulations, Molecular Dynamics