Molecular Dynamics Simulations of HLA-CW4-B2M-KIR2DL1 Protein and Homology Modeling of a Complex Associated with Psoriasis Disease (HLA-CW6-B 2M-KIR2DS1)
Almatarneh, M. H.; Alqaisi, A. M.; Ibrahim, E. K.; Kayed, G. G.; Hollett, J. W.
Show abstract
Molecular dynamics (MD) simulation was used to study the interactions of two immune proteins of HLA-Cw4-{beta}2m-KIR2DL1 complex with small peptide QYDDAVYKL (nine amino acids) in an aqueous solution. This study aims to gain a detailed information about the conformational changes and the dynamics of the complex. The right parameters and force field for performing the MD simulations that was needed to calibrate the complex structure were determined. The non-bonded interactions (Electrostatic and van der Waals contributions), H-bond formation, and salt bridges between the ligand HLA-Cw4 and the receptor KIR2DL1 were estimated using the obtained MD trajectories. The buried surface area due to binding was calculated to get insight into the causes of specificity of receptor to ligand and explains mutations experiment. The study concluded that {beta}2-microglobulin, one part of the complex, is not directly interacting with the peptide at the groove; therefore, it could be neglected from simulation. Our results showed that {beta}2-microglobulin does not have any significant effect on the dynamics of the 3D-structure of the complex. This project will help in understanding to optimize candidate drug design, a small peptide that disrupts the interaction, for the optimal biological effect.
Matching journals
The top 4 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- An insight into SARS-CoV-2 Membrane protein interaction with Spike, Envelope, and Nucleocapsid proteins 98%
- Investigating the role of N-terminal domain in phosphodiesterase 4B-inhibition by molecular dynamics simulation 98%
- Optimized structure of monoubiquitinated FANCD2 (human) at Lys 561: a theoretical approach 97%
Similar papers in this journal
- iBRAB: in silico based-designed Broad-spectrum Fab against H1N1 Influenza A Virus 97%
- Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8 97%
- Molecular Dynamics Study on the Effects of Charged Amino Acid Distribution Under low pH Condition to the Unfolding of Hen Egg White Lysozyme and Formation of Beta Strands. 96%
Similar papers in this journal
- Mechanistic insights into the deleterious role of nasu-hakola disease associated TREM2 variants 97%
- In Silico Analysis Predicting Effects of Deleterious SNPs of Human RASSF5 Gene on its Structure and Functions 96%
- Novel Peptide Inhibitor of Human Tumor Necrosis Factor-α has Antiarthritic Activity 95%
Similar papers in this journal
- Investigating the folding dynamics of NS2B protein of Zika virus 98%
- Structural dynamics of Zika Virus NS1 via a reductionist approach reveal the disordered nature of its beta roll domain in isolation 97%
- Microsecond simulations and CD spectroscopy reveals the intrinsically disordered nature of SARS-CoV-2 Spike-C-terminal cytoplasmic tail (residues 1242-1273) in isolation 97%
Similar papers in this journal
- Possible link between higher transmissibility of B.1.617 and B.1.1.7 variants of SARS-CoV-2 and increased structural stability of its spike protein and hACE2 affinity 97%
- Effect of Delta and Omicron mutations on the RBD-SD1 do-main of the Spike protein in SARS-CoV-2 and the Omicron mutations on RBD-ACE2 interface complex 97%
- Elucidation of Structural Mechanism of ATP Inhibition at the AAA1 Subunit of Cytoplasmic Dynein 1 Using a Chemical "Toolkit" 96%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.