Solvent Effect on the Structure and Properties of RGD Peptide (1FUV) at Body Temperature (310 K) Using Ab Initio Molecular Dynamics

Polymers

Khagendra Baral¹  Puja Adhikari¹  Bahaa Jawad¹  Wai-Yim Ching¹  Rudolf Podgornik² 

[1] Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA;School of Physical Sciences, Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China;

关键词: RGD peptide (1FUV);    ab initio molecular dynamics;    total bond order;    partial charge;    dielectric function;   

DOI  :  10.3390/polym13193434

来源: DOAJ

【 摘 要 】

The structure and properties of the arginine-glycine-aspartate (RGD) sequence of the 1FUV peptide at 0 K and body temperature (310 K) are systematically investigated in a dry and aqueous environment using more accurate ab initio molecular dynamics and density functional theory calculations. The fundamental properties, such as electronic structure, interatomic bonding, partial charge distribution, and dielectric response function at 0 and 310 K are analyzed, comparing them in dry and solvated models. These accurate microscopic parameters determined from highly reliable quantum mechanical calculations are useful to define the range and strength of complex molecular interactions occurring between the RGD peptide and the integrin receptor. The in-depth bonding picture analyzed using a novel quantum mechanical metric, the total bond order (TBO), quantifies the role played by hydrogen bonds in the internal cohesion of the simulated structures. The TBO at 310 K decreases in the dry model but increases in the solvated model. These differences are small but extremely important in the context of conditions prevalent in the human body and relevant for health issues. Our results provide a new level of understanding of the structure and properties of the 1FUV peptide and help in advancing the study of RGD containing other peptides.

【 授权许可】

Unknown