Biomaterial Database

Solvent accessibility and microenvironment in a bacterial protein proteinase inhibitor SSI (Streptomyces subtilisin inhibitor). 1980

Y Satow, and Y Watanabe, and Y Mitsui

Solvent accessibility (Lee, B. & Richards, F.M. (1971) J. Mol. Biol. 55, 379-400) was calculated for each atom of a bacterial protein proteinase inhibitor SSI (Streptomyces subtilisin inhibitor) based on crystallographic coordinates. Mainly based on this information, various chemical and spectroscopic (UV, Raman, NMR) observations made on the microenvironments of cystines, methionines, tryptophan, histidines, and tyrosines of SSI in solution were evaluated. Crystallographic data and the latter two sets of data were mainly at least qualitatively consistent with each other. These data include (1) the conformation of the two disulfide bridges, (2) the flexibility of the three methionyl side chains, (3) the extent of exposure of the indole ring of a tryptophan, (4) the environment of the two histidines, (5) the environment of the tyrosines, and (6) the hydrogen-deuterium exchangeability of peptide NH's. However, the extents of exposure of tyrosines deduced by solvent perturbation UV difference spectroscopy were significantly larger than those based on solvent accessibility calculations. Possible reasons for this discrepancy are discussed.

UI	MeSH Term	Description	Entries
D008715	Methionine	A sulfur-containing essential L-amino acid that is important in many body functions.	L-Methionine,Liquimeth,Methionine, L-Isomer,Pedameth,L-Isomer Methionine,Methionine, L Isomer
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
D011487	Protein Conformation	The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).	Conformation, Protein,Conformations, Protein,Protein Conformations
D002621	Chemistry	A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.
D004220	Disulfides	Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.	Disulfide
D006639	Histidine	An essential amino acid that is required for the production of HISTAMINE.	Histidine, L-isomer,L-Histidine,Histidine, L isomer,L-isomer Histidine
D001426	Bacterial Proteins	Proteins found in any species of bacterium.	Bacterial Gene Products,Bacterial Gene Proteins,Gene Products, Bacterial,Bacterial Gene Product,Bacterial Gene Protein,Bacterial Protein,Gene Product, Bacterial,Gene Protein, Bacterial,Gene Proteins, Bacterial,Protein, Bacterial,Proteins, Bacterial
D012997	Solvents	Liquids that dissolve other substances (solutes), generally solids, without any change in chemical composition, as, water containing sugar. (Grant & Hackh's Chemical Dictionary, 5th ed)	Solvent
D013381	Subtilisins	A family of SERINE ENDOPEPTIDASES isolated from Bacillus subtilis. EC 3.4.21.-	Alcalase,AprA-Subtilisin,Bacillus amyloliquefaciens Serine Protease,Bacillus subtilis Alkaline Proteinase,Carlsberg Subtilisin,Maxatase,Nagarse,Novo Alcalase,Profezim,Protease VII,Subtilisin 72,Subtilisin A,Subtilisin BPN',Subtilisin Carlsberg,Subtilisin DY,Subtilisin E,Subtilisin GX,Subtilisin Novo,Subtilopeptidase A,Alcalase, Novo,AprA Subtilisin,Subtilisin, Carlsberg
D013499	Surface Properties	Characteristics or attributes of the outer boundaries of objects, including molecules.	Properties, Surface,Property, Surface,Surface Property