Biomaterial Database

Environmental Effects on Salt Bridge Stability in the Protein-Protein Interface: The Case of Hen Egg-White Lysozyme and Its Antibody, HyHEL-10. 2021

Ryo Okajima, and Shuichi Hiraoka, and Takefumi Yamashita

Department of Basic Science, Graduate School of Arts and Sciences, the University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.

We studied the stability of two salt bridges between hen egg-white lysozyme (HEL) and its antibody, HyHEL-10, by using molecular dynamics simulations. It was observed that one salt bridge, D32H-K97Y, was stable, whereas the other, D99H-K97Y, was not. To understand this difference, we compared several reduced salt bridge models that incorporated the salt bridges and nearby residues. The results showed the importance of nearby residues, especially Y33H and W98H. Furthermore, to understand the effects of nearby salt bridges, we investigated two mutants, D32HA and D99HA. We found that the D32HA mutation considerably stabilized the D99H-K97Y salt bridge. The reduced model analysis indicated that this can be largely attributed to a conformational change of the main chain.

UI	MeSH Term	Description	Entries
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D009113	Muramidase	A basic enzyme that is present in saliva, tears, egg white, and many animal fluids. It functions as an antibacterial agent. The enzyme catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrin. EC 3.2.1.17.	Lysozyme,Leftose,N-Acetylmuramide Glycanhydrolase,Glycanhydrolase, N-Acetylmuramide,N Acetylmuramide Glycanhydrolase
D002645	Chickens	Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.	Gallus gallus,Gallus domesticus,Gallus gallus domesticus,Chicken
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D000936	Antigen-Antibody Complex	The complex formed by the binding of antigen and antibody molecules. The deposition of large antigen-antibody complexes leading to tissue damage causes IMMUNE COMPLEX DISEASES.	Immune Complex,Antigen-Antibody Complexes,Immune Complexes,Antigen Antibody Complex,Antigen Antibody Complexes,Complex, Antigen-Antibody,Complex, Immune,Complexes, Antigen-Antibody,Complexes, Immune