Molecular dynamics simulations and density functional theory studies of NALMA and NAGMA dipeptides

<div><p>Classical molecular dynamics (MD) simulations using fixed charged force field (AMBER ff03) and density functional theory method using the M05-2X/6-31G^∗∗ level of theory have been used to investigate the plasticity of the hydrogen bond formed between dipeptides of N-Acetyl-Leucine-MethylAmide (NALMA), N-Acetyl-Glycine-MethylAmide (NAGMA), and vicinity of water molecules at temperature of 300 K. We have noticed that 2–3 water molecules contribute to change in the conformations of dipeptides NAGMA and NALMA. The self-assembly of 11 water molecules leads to the formation of water bridge at vicinity of the dipeptides and it constrain the conformations of dipeptides. We have found that the energy balance between breaking of the C = O…H–N H bonds and the formation of the C = O…H–O (wat) H bonds may be one of the determining factors to control the dynamics of the folding process of protein molecules.</p> </div

Structure, stability and water permeation of ([D-Leu-L-Lys-(D-Gln-L-Ala)₃]) cyclic peptide nanotube: a molecular dynamics study

<p>The structural stability of 8 × ([D-Leu-L-Lys-(D-Gln-L-Ala)₃]) cyclic peptide nanotube (CPN) in water and different phospholipid bilayers were explored by 100 ns independent molecular dynamics (MD) simulations. The role of non-bonded interaction energy between the side and main chains of cyclic peptide rings in different membrane environments assessed, wherein the repulsive electrostatic interaction energy between neighbouring cyclic peptide rings was found adequate to break hydrogen bond energy thereby to crumple CPN. Further, the water permeation across the CPN channel was studied in four types of phospholipid bilayers- DMPG (1,2-Dimyristoyl-sn-glycero-3-phosphorylglycerol), DMPS (1,2-Dimyristoyl-sn-glycero-3-phosphoserine), POPC (1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and POPE (1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) from MD simulations. DMPS membrane shows higher non-bonded interaction energies (−1913.06 kJ/mol of electrostatic interaction energy and −994.13 kJ/mol of van der Waals interaction energy) with CPN due to the presence of polar molecules in lipid structure. Thusly, the non-bonded interaction energies were essential towards the stability of CPN than hydrogen bonds between the nearby cyclic peptides. The result also reveals the role of side chains, hydrogen bonds and non-bonded interaction energies in an aqueous environment. The diffusion coefficient of water obtained from means square deviation calculation shows similar coefficients irrespective of the lipid surroundings. However, the permeation coefficients demonstrate water flow in the channel relies upon the environment.</p

Supplementary Material.pdf

<p><b><u>Supplementary Information</u></b></p> <p><b>Structure, Stability and water permeation of ([D-Leu-L-Lys-(D-Gln-L-Ala)₃]) cyclic peptide nanotube: A molecular dynamics study</b></p> <p>Nikhil Maroli¹, Ponmalai Kolandaivel^2*</p> <p>1. Computational Biology Division,DRDO BU CLS,Coimbatore-641046,Tamil Nadu,INDIA</p> <p>2.Department of Physics, Bharathiar University, Coimbatore, Tamil Nadu, INDIA</p> <p> </p> <p>*Corresponding author:</p> <p>E-mail address: [email protected]</p><p><br></p><p>https://doi.org/10.1080/08927022.2017.1366653<br></p