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The influence of flanking secondary structures on amino Acid content and typical lengths of 3/10 helices.

ABSTRACT: We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges-regions situated between any of two major elements of secondary structure (alpha helices and beta strands)-containing a pure random coil were compared with connecting bridges containing 3/10 helices. We included discovered trends in the original "VVTAK Connecting Bridges" algorithm, which is able to predict more probable conformation for a given connecting bridge. The highest number of significant differences in amino acid usage was found between 3/10 helices containing bridges connecting two beta strands (they have increased Phe, Tyr, Met, Ile, Leu, Val, and His usages but decreased usages of Asp, Asn, Gly, and Pro) and those without 3/10 helices. The typical (most common) length of 3/10 helices situated between two beta strands and between beta strand and alpha helix is equal to 5 amino acid residues. The preferred length of 3/10 helices situated between alpha helix and beta strand is equal to 3 residues. For 3/10 helices situated between two alpha helices, both lengths (3 and 5 amino acid residues) are typical.

SUBMITTER: Khrustalev VV

PROVIDER: S-EPMC4211214 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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The influence of flanking secondary structures on amino Acid content and typical lengths of 3/10 helices.

Khrustalev Vladislav Victorovich VV Barkovsky Eugene Victorovich EV Khrustaleva Tatyana Aleksandrovna TA

International journal of proteomics 20141013

We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges-regions situated between any of two major elements of secondary structure (alpha helices and beta strands)-containing a pure random coil were compared with connecting bridges containing 3/10 helices. We included discovered trends in the original "VVTAK Connecting Bridges" algorithm, which is able to predict more probable conformation for a ...[more]

PMID: 25371821

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Project description:The unique physiochemical properties and multiscale organization of layered materials draw the attention of researchers across a wide range of scientific disciplines. Layered structures are commonly found in diverse biological systems where they fulfill various functions. A prominent example of layered biological materials is the organization of proteins and polypeptides into the archetypal aggregated amyloidal structures. While the organization of proteins into amyloid structures was initially associated with various degenerative disorders, it was later revealed that proteins not related to any disease could also form identical layered assemblies. Thus, it appears that the ability of peptides and proteins to produce amyloid-like aggregates represents a generic property of polyamides to assemble into higher order fibrillar structures. In the aggregated state, the peptide backbone forms ?-sheet structures which are further organized into layered arrangements. We have recently extended the identified amyloidogenic building blocks to include not only peptides or proteins, but also single amino acids and other metabolites. High resolution spectroscopy and crystallography analyses confirm the clear potential of amino acids and other metabolites to form layered amyloid-like aggregates showing biophysical and biochemical properties similar to protein amyloids. Therefore, the generic propensity of peptides and proteins backbones to assemble into layered organizations may emanate from their basic building block, the amino acid. In this Account, we aim to introduce the concept of supramolecular ?-sheet organization of single amino acids and to present an analysis of their layered-structure organization based on single crystal structures. We demonstrate that, despite the different side-chains that considerably vary in their chemical properties, all coded amino acids display a layer-like assembly stabilized by ?-amine to ?-carboxyl H-bonds, resembling supramolecular ?-sheet structures, while the side-chains determine the higher order organization of the layers. Our work presents the first analysis of the ?-sheet propensity of single amino acids in their unbound form, indicating an evolutionary predisposition. We classify the amino acids ?-sheet propensity on the basis of the interlayer separation distance in the crystal packing, which correlates well with previously reported classifications based on various criteria, such as hydrophobicity, steric bulkiness, and folding. In addition, we demonstrate that the relative direction of ?-amine to ?-carboxyl H-bonding pattern provides critical insights regarding the stabilization of parallel versus antiparallel ?-sheet structures by the various amino acids. Taken together, our analysis of amino acid crystals provides substantial information regarding protein folding and dynamics and could serve as basic rules set for the design of potential building blocks for molecular self-assembly to produce functional materials of tunable properties, an important objective of bottom-up nanotechnology.

Dataset Information

The influence of flanking secondary structures on amino Acid content and typical lengths of 3/10 helices.

Publications

The influence of flanking secondary structures on amino Acid content and typical lengths of 3/10 helices.

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