Abstract
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.
Highlights
Biomolecular materials containing the arginine-glycine-aspartate (RGD) sequence are always at the center of biophysics research in their application such as in the bone scaffold, synthesis, and regeneration of tissue and cartilage [1,2], in imaging as radiotracers [3,4,5,6], for cancer therapy [7,8,9], and in targeted drug delivery [10,11,12,13,14,15]
The short- and long-range interactions are crucial for the molecular recognition and self-assembly of biological macromolecules, and determining the microscopic parameters such as partial charge and frequency-dependent dielectric functions based on more accurate quantum mechanical calculation will facilitate the fundamental understanding of electrostatic, polar, and van der Waals-London dispersion interaction in biologicalmolecules
Atomic orbitals in the basis expansion enables us to quantify the charge transfer and interFrom the calculated value of Q* the charge transfer between the ions due to atomic atomic bonding via effective charge (Q*) on each atom and bond order (BO) value between interaction can be quantified in terms of the partial charge (PC)
Summary
Biomolecular materials containing the arginine-glycine-aspartate (RGD) sequence are always at the center of biophysics research in their application such as in the bone scaffold, synthesis, and regeneration of tissue and cartilage [1,2], in imaging as radiotracers [3,4,5,6], for cancer therapy [7,8,9], and in targeted drug delivery [10,11,12,13,14,15]. The need for AIMD simulation in the study of dry and aqueous solvated peptide/protein over classical MD has been repeatedly recognized [28,29,30,31] and a more accurate AIMD calculation with a sufficiently large number of water molecules is highly desirable for a complete understanding of 1FUV aqueous solvation Experimental techniques such as nuclear magnetic resonance (NMR), surfaceenhanced Raman spectroscopy, X-ray photoelectron spectroscopy, etc., are used to investigate the structure and properties of RGD containing peptides [16,32,33,34,35], the experimental studies involving 1FUV are scant. The main part is the result and discussion section, in which we discuss our findings and articulate the future prospects for applying AIMD to other complex biomolecular systems
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