3D interaction homology: The hydropathic interaction environments of even alanine are diverse and provide novel structural insight.

Ahmed, Mostafa H; Catalano, Claudio; Portillo, Samuel C; Safo, Martin K; Neel Scarsdale, J; Kellogg, Glen E

Ahmed, Mostafa H; Catalano, Claudio; Portillo, Samuel C; Safo, Martin K; Neel Scarsdale, J; Kellogg, Glen E.

Afiliación

Ahmed MH; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA; Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA.
Catalano C; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA; Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA.
Portillo SC; Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.
Safo MK; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA; Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA.
Neel Scarsdale J; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA; Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.
Kellogg GE; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA; Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA; Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA

J Struct Biol ; 207(2): 183-198, 2019 08 01.

Article en En | MEDLINE | ID: mdl-31112746

RESUMEN

Analyses of the hydropathic environments of protein amino acid residues reveal structural information on multiple levels. The interactions made by each residue are the basis for sidechain (rotamer) conformation and ultimately for secondary, tertiary and even quaternary protein structure. By identifying and characterizing the interactions for each residue type, we are developing a basis set of environmental data that can be used to understand protein structure. This work focuses alanine and its roles. We calculated and analyzed separately backbone-to-environment and sidechain-to-environment 3D maps for over 57,000 alanines that, with respect to hydrophobic and polar interactions, show the environment around each. After binning by backbone Ï and ψ angles, we clustered each bin with k-means based on calculated map similarities between map-map pairs. Four bins were examined in detail: one in the ß-pleat region, two in the right-hand α-helix (RHα) region and one in the left-hand α-helix region of the Ramachandran plot. All regions indicated a common map motif of hydrophobic-hydrophobic interactions along the CA-CB axis, accounting for 62% in the ß-pleat bin, about one-third in the two RHα bins and 42% in the LHα bin. Another shared motif shows no interactions along the CA-CB axis; this was uncommon (8%) in ß-pleat, but >30% elsewhere. The maps calculated for the two RHα bins are extremely similar (pairwise >0.9787), which suggests that the hydropathic interaction sets or motifs found around each residue are conserved. Altogether, these results are integral to a new paradigm for understanding protein structure and function.

Asunto(s)

Alanina/química; Aminoácidos/química; Conformación Proteica en Hélice alfa; Conformación Proteica; Alanina/genética; Secuencias de Aminoácidos/genética; Aminoácidos/genética; Interacciones Hidrofóbicas e Hidrofílicas; Conformación Molecular; Conformación Proteica en Lámina beta/genética; Estructura Cuaternaria de Proteína/genética; Estructura Secundaria de Proteína/genética; Estructura Terciaria de Proteína/genética

Palabras clave

Alanine; Hydropathic interaction environment; Protein structure; Ramachandran analysis; Secondary structure

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Conformación Proteica / Alanina / Conformación Proteica en Hélice alfa / Aminoácidos Idioma: En Revista: J Struct Biol Asunto de la revista: BIOLOGIA MOLECULAR Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos

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