Abstract
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).
Highlights
In a previous study of α-helices’ nanoenvironments, we presented data which clearly identify the most relevant protein structure attributes/descriptors/parameters fully describing the corresponding nanoenvironment [1]
In the case of proteins designated as all-α, the following descriptors had more than 80% of cases for p-value being lower than 1e-6: “hydrogen bond between main chain main chain atoms” (85.71%), “hydrogen bond between main chain main chain atoms-weighted neighbor averages by distance” (85.71%) and “hydrogen bond between main chain main chain” atoms weighted neighbor averages at surface” (82.85%)
Considering the most restrictive consensus for definition of secondary structure element, i.e. the one with coinciding/equivalent PDB, DSSP and Stride definitions, and no redundancy, there are 106,651 β-sheet elements in the all-β dataset and 167,080 β-sheet elements in (α + β) + (α / β) dataset
Summary
In a previous study of α-helices’ nanoenvironments, we presented data which clearly identify the most relevant protein structure attributes/descriptors/parameters fully describing the corresponding nanoenvironment [1]. Considering that the total number of β-sheets found in the current PDB is far greater than the total number of α-helices in all proteins, we are interested in investigating the differences between α-helical and β-sheet nanoenvironments and whether the precision and coverage of defining respective nanoenvironments are greater in the latter case. It is important to distinguish the two flavors of the β-sheets; they could be parallel or anti-parallel. Β-sheets could even appear (rarely) in a form where only one strand exists, as one could verify in protein structures described in PDB entry: 1A2J. Single-stranded β-sheets are identified by code number 0 [2]
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have