scholarly journals Towards Symmetry-Based Explanation of (Approximate) Shapes of Alpha-Helices and Beta-Sheets (and Beta-Barrels) in Protein Structure

Symmetry ◽  
2012 ◽  
Vol 4 (1) ◽  
pp. 15-25 ◽  
Author(s):  
Jaime Nava ◽  
Vladik Kreinovich
Keyword(s):  
Protein Structure ◽  
Beta Sheets ◽  
Alpha Helices ◽  
Beta Barrels

scholarly journals Analysis of Three-Dimensional Protein Images

1997 ◽  
Vol 7 ◽  
pp. 125-159 ◽  
Author(s):  
L. Leherte ◽  
J. Glasgow ◽  
K. Baxter ◽  
E. Steeg ◽  
S. Fortier
Keyword(s):  
Protein Structure ◽  
Structure Prediction ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Beta Sheets ◽  
Scene Analysis ◽  
Certainty Factor ◽  
Alpha Helices ◽  
Medium Resolution ◽  
Fundamental Goal

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.

scholarly journals Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins

1993 ◽  
Vol 90 (23) ◽  
pp. 10962-10966 ◽  
Author(s):  
K M Pan ◽  
M Baldwin ◽  
J Nguyen ◽  
M Gasset ◽  
A Serban ◽  
...  
Keyword(s):  
Chemical Modification ◽  
Prion Protein ◽  
Conformational Transition ◽  
Prion Proteins ◽  
Limited Proteolysis ◽  
Alpha Helix ◽  
Beta Sheets ◽  
Cellular Prion Protein ◽  
Beta Sheet ◽  
Alpha Helices

Prions are composed largely, if not entirely, of prion protein (PrPSc in the case of scrapie). Although the formation of PrPSc from the cellular prion protein (PrPC) is a post-translational process, no candidate chemical modification was identified, suggesting that a conformational change features in PrPSc synthesis. To assess this possibility, we purified both PrPC and PrPSc by using nondenaturing procedures and determined the secondary structure of each. Fourier-transform infrared (FTIR) spectroscopy demonstrated that PrPC has a high alpha-helix content (42%) and no beta-sheet (3%), findings that were confirmed by circular dichroism measurements. In contrast, the beta-sheet content of PrPSc was 43% and the alpha-helix 30% as measured by FTIR. As determined in earlier studies, N-terminally truncated PrPSc derived by limited proteolysis, designated PrP 27-30, has an even higher beta-sheet content (54%) and a lower alpha-helix content (21%). Neither PrPC nor PrPSc formed aggregates detectable by electron microscopy, while PrP 27-30 polymerized into rod-shaped amyloids. While the foregoing findings argue that the conversion of alpha-helices into beta-sheets underlies the formation of PrPSc, we cannot eliminate the possibility that an undetected chemical modification of a small fraction of PrPSc initiates this process. Since PrPSc seems to be the only component of the "infectious" prion particle, it is likely that this conformational transition is a fundamental event in the propagation of prions.

scholarly journals In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Hafiz Ishfaq Ahmad ◽  
Gulnaz Afzal ◽  
Adil Jamal ◽  
Shumaila Kiran ◽  
Musarrat Abbas Khan ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Alpha Helix ◽  
Beta Sheets ◽  
Random Coil ◽  
Functional Study ◽  
Motif Analysis ◽  
Alpha Helices ◽  
Random Coils ◽  
Metabolic Reactions ◽  
Exogenous Compounds

Cytochrome (CYP) enzymes catalyze the metabolic reactions of endogenous and exogenous compounds. The superfamily of enzymes is found across many organisms, regardless of type, except for plants. Information was gathered about CYP2D enzymes through protein sequences of humans and other organisms. The secondary structure was predicted using the SOPMA. The structural and functional study of human CYP2D was conducted using ProtParam, SOPMA, Predotar 1.03, SignalP, TMHMM 2.0, and ExPASy. Most animals shared five central motifs according to motif analysis results. The tertiary structure of human CYP2D, as well as other animal species, was predicted by Phyre2. Human CYP2D proteins are heavily conserved across organisms, according to the findings. This indicates that they are descended from a single ancestor. They calculate the ratio of alpha-helices to extended strands to beta sheets to random coils. Most of the enzymes are alpha-helix, but small amounts of the random coil were also found. The data were obtained to provide us with a better understanding of mammalian proteins’ functions and evolutionary relationships.

Mechanical unfolding of alpha- and beta-helical protein motifs

Soft Matter ◽  
2019 ◽  
Vol 15 (6) ◽  
pp. 1243-1252 ◽  
Author(s):  
Elizabeth P. DeBenedictis ◽  
Sinan Keten
Keyword(s):  
Energy Dissipation ◽  
Hydrogen Bonds ◽  
Beta Sheets ◽  
Height Ratio ◽  
Alpha Helices ◽  
Protein Motifs ◽  
Loading Direction ◽  
Out Of Plane ◽  
Helical Protein

Alpha-helices and beta-sheets are the two most common secondary motifs in proteins. Beta-helices combine features of both motifs to perform a wide variety of functions. Possessing a larger width to height ratio, beta-helices resist unfolding by rotating to larger angles with respect to the loading direction, resulting in hydrogen bonds being ruptured in shear or out of plane peeling rather than in-plane peeling. This allows beta-helices to achieve greater energy dissipation per residue than alpha-helices.

scholarly journals Proteomics Computational Analyses Suggest that the Envelope Glycoproteins of Segmented Jingmen Flavi-Like Viruses Are Class II Viral Fusion Proteins (β-Penetrenes) with Mucin-Like Domains

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 260 ◽  
Author(s):  
Courtney Garry ◽  
Robert Garry
Keyword(s):  
Fusion Proteins ◽  
Domain Architecture ◽  
Class Ii ◽  
Structural Features ◽  
Beta Sheets ◽  
Viral Fusion ◽  
Alpha Helices ◽  
Worldwide Distribution ◽  
Viral Fusion Proteins ◽  
Computational Analyses

Jingmen viruses are newly described segmented flavi-like viruses that have a worldwide distribution in ticks and have been associated with febrile illnesses in humans. Computational analyses were used to predict that Jingmen flavi-like virus glycoproteins have structural features of class II viral fusion proteins, including an ectodomain consisting of beta-sheets and short alpha-helices, a fusion peptide with interfacial hydrophobicity and a three-domain architecture. Jingmen flavi-like virus glycoproteins have a sequence enriched in serine, threonine, and proline at the amino terminus, which is a feature of mucin-like domains. Several of the serines and threonines are predicted be modified by the addition of O-linked glycans. Some of the glycoproteins are predicted to have an additional mucin-like domain located prior to the transmembrane anchor, whereas others are predicted to have a stem consisting of two alpha-helices. The flavivirus envelope protein and Jingmen flavi-virus glycoproteins may have diverged from a common class II precursor glycoprotein with a mucin-like domain or domains acquired after divergence.

scholarly journals Alloreactive cytotoxic T lymphocytes recognize epitopes determined by both the alpha helices and beta sheets of the class I peptide binding site.

1992 ◽  
Vol 175 (3) ◽  
pp. 821-829 ◽  
Author(s):  
H D Hunt ◽  
T I Munitz ◽  
L R Pease
Keyword(s):  
Amino Acid ◽  
T Lymphocytes ◽  
Cytotoxic T Lymphocytes ◽  
Peptide Binding ◽  
Beta Sheets ◽  
Class I ◽  
Alpha Helices ◽  
L Cells ◽  
Strong Anchor ◽  
Antigen Presenting

A chimeric class I glycoprotein was created to investigate the functional contribution of the alpha helices and the beta-pleated sheets in forming the antigen recognition site (ARS) of antigen-presenting molecules. This novel molecule was generated by replacing the DNA sequences encoding the alpha helices of the Ld gene with the corresponding sequences from the Kb gene. Serologic analysis of transfected L cells that expressed the chimeric molecule (Kb alpha Ld beta) revealed that the engineered class I glycoprotein retains two conformational epitopes associated with the alpha helices of Kb, as defined by monoclonal antibodies K10.56 and 28-13-3. These results demonstrate that the alpha helices of Kb can associate with the beta-pleated sheets of Ld to form a stable structure, which is expressed on the cell surface. To address the role of the alpha helices of the ARS in determining T cell crossreactivity, alloreactive cytotoxic T lymphocytes (CTL) were used to analyze L cells expressing Kb alpha Ld beta. CTL raised against Kb or Ld as alloantigens showed little, if any, ability to lyse L cells expressing Kb alpha Ld beta. Thus, alloreactive CTL did not recognize structures determined by the alpha helices alone or by the beta sheets of the ARS alone. However, bulk and cloned alloreactive CTL that were generated against the mutant Kb glycoprotein Kbm8 reacted strongly with Kb alpha Ld beta. In addition to the Kb alpha helices, the Kbm8 ARS shares a single polymorphic amino acid at position 24 with Kb alpha Ld beta. Amino acid 24 is located on the beta 2 strand that forms part of the floor of the ARS and has been identified as a component of pocket B in the HLA class I ARS. The substitution of Glu to Ser at this position was shown previously to be the central determinant of the Kbm8 mutant alloantigenicity. The functional significance of this position in determining crossreactivity between bm8 and Kb alpha Ld beta identifies pocket B as a strong anchor for allogenic self-peptides. These findings demonstrate that determinants recognized by CTL on class I alloantigens are formed by interactions involving both the alpha helices and beta sheets of the ARS. These interactions are best explained by the influence of the alpha helices and beta sheets on the peptide-binding properties of these antigen-presenting molecules.

scholarly journals Building blocks of protein structures – Physics meets Biology

2020 ◽  
Author(s):  
Tatjana Skrbic ◽  
Amos Maritan ◽  
Achille Giacometti ◽  
George D. Rose ◽  
Jayanth R. Banavar
Keyword(s):  
Protein Structures ◽  
Building Blocks ◽  
Vital Role ◽  
Beta Sheets ◽  
Sequence Information ◽  
Alpha Helices ◽  
Solvent Interactions ◽  
Guiding Principle ◽  
Amino Acid Sequence Information

The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry of the building blocks of protein structures, alpha-helices and strands assembled into beta-sheets, with no adjustable parameters, no amino acid sequence information, and no chemistry. There is an almost perfect fit between the dictates of mathematics and physics and the rules of quantum chemistry. Our theory establishes an energy landscape that channels protein evolution by providing sequence-independent platforms for elaborating sequence-dependent functional diversity. Our work highlights the vital role of discreteness in life and has implications for the creation of artificial life and on the nature of life elsewhere in the cosmos.

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