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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

A comparison between internal protein nanoenvironments of alpha-helices and beta-sheets

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Author(s):
Mazoni, Ivan [1] ; Salim, Jose Augusto [2] ; de Moraes, Fabio Rogerio [3] ; Borro, Luiz [4] ; Neshich, Goran [1]
Total Authors: 5
Affiliation:
[1] Embrapa Agr Informat, Computat Biol Res Grp, Campinas, SP - Brazil
[2] Univ Sao Paulo, Res Ctr Biodivers & Comp BIOCOMP, Polytech Sch, Sao Paulo - Brazil
[3] Sao Paulo State Univ Unesp, Dept Phys, Inst Biosci Languages & Exact Sci IBILCE, Ribeirao Preto, SP - Brazil
[4] CPqD Fdn, IoT & AI Solut, Campinas, SP - Brazil
Total Affiliations: 4
Document type: Journal article
Source: PLoS One; v. 15, n. 12 DEC 30 2020.
Web of Science Citations: 0
Abstract

Secondary structure elements are generally found in almost all protein structures revealed so far. In general, there are more beta-sheets than alpha helices found inside the protein structures. For example, considering the PDB, DSSP and Stride definitions for secondary structure elements and by using the consensus among those, we found 60,727 helices in 4,376 chains identified in all-alpha structures and 129,440 helices in 7,898 chains identified in all-alpha and alpha + beta structures. For beta-sheets, we identified 837,345 strands in 184,925 beta-sheets located within 50,803 chains of all-beta structures and 1,541,961 strands in 355,431 beta-sheets located within 86,939 chains in all-beta and alpha + beta structures (data extracted on February 1, 2019). In this paper we would first like to address a full characterization of the nanoenvironment found at beta sheet locations and then compare those characteristics with the ones we already published for alpha helical secondary structure elements. For such characterization, we use here, as in our previous work about alpha helical nanoenvironments, set of STING protein structure descriptors. As in the previous work, we assume that we will be able to prove that there is a set of protein structure parameters/attributes/descriptors, which could fully describe the nanoenvironment around beta sheets and that appropriate statistically analysis will point out to significant changes in values for those parameters when compared for loci considered inside and outside defined secondary structure element. Clearly, while the univariate analysis is straightforward and intuitively understood, it is severely limited in coverage: it could be successfully applied at best in up to 25% of studied cases. The indication of the main descriptors for the specific secondary structure element (SSE) by means of the multivariate MANOVA test is the strong statistical tool for complete discrimination among the SSEs, and it revealed itself as the one with the highest coverage. The complete description of the nanoenvironment, by analogy, might be understood in terms of describing a key lock system, where all lock mini cylinders need to combine their elevation (controlled by a matching key) to open the lock. The main idea is as follows: a set of descriptors (cylinders in the key-lock example) must precisely combine their values (elevation) to form and maintain a specific secondary structure element nanoenvironment (a required condition for a key being able to open a lock). (AU)

FAPESP's process: 18/25327-6 - Updating sting platform and its relational database for complementing of a dictionary containing principal descriptors that characterize the ten most studied internal protein nano environments
Grantee:Goran Nesic
Support type: Regular Research Grants