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Made available in DSpace on 2021-06-25T10:48:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-12-01 Secondary structure elements are generally found in almost all protein structures revealed so far. In general, there are more β-sheets than α 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-α structures and 129,440 helices in 7,898 chains identified in all-α and α + β structures. For β-sheets, we identified 837,345 strands in 184,925 β-sheets located within 50,803 chains of all-β structures and 1,541,961 strands in 355,431 β-sheets located within 86,939 chains in all-β and α + β 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). Computational Biology Research Group Embrapa Agricultural Informatics Research Center on Biodiversity and Computing (BIOCOMP) Polytechnic School of the University of SãoPaulo (USP) Physics Department Institute of Biosciences Languages and ExactSciences (IBILCE) São Paulo State University (Unesp) IoT & AI Solutions CPqD Foundation Physics Department Institute of Biosciences Languages and ExactSciences (IBILCE) São Paulo State University (Unesp)

Protein secondary structure elements (PSSEs) such as [alfa]-helices, [beta]-strands, and turns are the primary building blocks of the tertiary protein structure. Our primary interest here is to reveal the characteristics of the nanoenvironment formed by both PSSEs and their surrounding amino acid residues (AARs), which might contribute to the general understanding of how proteins fold. Made available in DSpace on 2018-07-21T01:04:12Z (GMT). No. of bitstreams: 1 journal.pone.0200018.pdf: 6561301 bytes, checksum: 285175de95eedf35d7adc5690d1db4ce (MD5) Previous issue date: 2018-07-20 Artigo e0200018.

This article is intended to show how Sting Millennium Suite of programs can be useful in the study of protein structure and analysis of its function, emphasizing recent improvement introduced to SMS. The program has extensive built-in instructions and detailed easy-to-use help which user is invited to consult before and during SMS use. Made available in DSpace on 2011-04-09T17:36:16Z (GMT). No. of bitstreams: 1 sting.pdf: 910463 bytes, checksum: 439d25ece2ce0fd8603515e643301da2 (MD5) Previous issue date: 2005-08-04 Na publicação: Paula R Kuser.