A New Type ofφ,ψRepresentation of the Protein Tertiary Structure and the Analysis of the Amino Acid Preferences for Specific Locations at Type-IIβ-Turn by Using 8000 Possible Kinds of Amino Acid Residues

Halophilic (literally salt-loving) archaea are a highly evolved group of organisms that are uniquely able to survive in and exploit hypersaline environments. In this review, we examine the potential interplay between fluctuations in environmental salinity and the primary sequence and tertiary structure of halophilic proteins. The proteins of halophilic archaea are highly adapted and magnificently engineered to function in an intracellular milieu that is in ionic balance with an external environment containing between 2 and 5 M inorganic salt. To understand the nature of halophilic adaptation and to visualize this interplay, the sequences of genes encoding the L11, L1, L10, and L12 proteins of the large ribosome subunit and Mn/Fe superoxide dismutase proteins from three genera of halophilic archaea have been aligned and analyzed for the presence of synonymous and nonsynonymous nucleotide substitutions. Compared to homologous eubacterial genes, these halophilic genes exhibit an inordinately high proportion of nonsynonymous nucleotide substitutions that result in amino acid replacement in the encoded proteins. More than one-third of the replacements involve acidic amino acid residues. We suggest that fluctuations in environmental salinity provide the driving force for fixation of the excessive number of nonsynonymous substitutions. Tinkering with the number, location, and arrangement of acidic and other amino acid residues influences the fitness (i.e., hydrophobicity, surface hydration, and structural stability) of the halophilic protein. Tinkering is also evident at halophilic protein positions monomorphic or polymorphic for serine; more than one-third of these positions use both the TCN and the AGY serine codons, indicating that there have been multiple nonsynonymous substitutions at these positions. Our model suggests that fluctuating environmental salinity prevents optimization of fitness for many halophilic proteins and helps to explain the unusual evolutionary divergence of their encoding genes.

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Model of a folded polypeptide chain

Proceedings of the Royal Society of London Series B Biological Sciences ◽

10.1098/rspb.1950.0023 ◽

1950 ◽

Vol 137 (886) ◽

pp. 79-79

Keyword(s):

Amino Acid ◽

Polypeptide Chain ◽

Molecular Model ◽

Polymer Chains ◽

Side Chains ◽

Amino Acid Residues ◽

Infra Red ◽

New Type ◽

Folded Proteins ◽

Red Radiation

The models on view in the ante-room show a way of folding a polypeptide chain which is consistent with some observations we have recently made with polarized infra-red radiation (Ambrose & Hanby 1949; Ambrose, Elliott & Temple 1949). The α -folded proteins, keratin, myosin and tropomyosin, have been found when oriented to show greater absorption of the N-H frequency when the electric vector of the absorbed radiation is in the direction of the fibre axis, hence the N-H bond must be preferentially oriented in this direction. A study of models has suggested that the only likely folding of the polypeptide chain consistent with this fact involves a seven-membered ring containing two amino-acid residues; the ring is completed by hydrogen bonds: A new type of atomic model which has been developed in our laboratories has been used. The scale is 0·8 in. to the Angstrom unit. The valency links, while allowing free rotation about single co-valent bonds, also allow some distortion of the bond angles when strains occur but are strong enough to allow long polymer chains to be built. The molecular model exhibited shows twenty-four amino-acid residues, with side chains on one side of the back-bone, representative of those occurring in myosin; the side chains on the other side have been removed for clearness and their positions indicated by single carbon atoms.

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Identification of Amino Acid Residues in CD81 Critical for Interaction with Hepatitis C Virus Envelope Glycoprotein E2

Journal of Virology ◽

10.1128/jvi.74.8.3642-3649.2000 ◽

2000 ◽

Vol 74 (8) ◽

pp. 3642-3649 ◽

Cited By ~ 165

Author(s):

Adrian Higginbottom ◽

Elizabeth R. Quinn ◽

Chiung-Chi Kuo ◽

Mike Flint ◽

Louise H. Wilson ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Amino Acid ◽

Envelope Glycoprotein ◽

Tertiary Structure ◽

Antibody Binding ◽

Viral Envelope ◽

Amino Acid Residues ◽

Virus Envelope ◽

Glycoprotein E2

ABSTRACT Human CD81 has been previously identified as the putative receptor for the hepatitis C virus envelope glycoprotein E2. The large extracellular loop (LEL) of human CD81 differs in four amino acid residues from that of the African green monkey (AGM), which does not bind E2. We mutated each of the four positions in human CD81 to the corresponding AGM residues and expressed them as soluble fusion LEL proteins in bacteria or as complete membrane proteins in mammalian cells. We found human amino acid 186 to be critical for the interaction with the viral envelope glycoprotein. This residue was also important for binding of certain anti-CD81 monoclonal antibodies. Mutating residues 188 and 196 did not affect E2 or antibody binding. Interestingly, mutation of residue 163 increased both E2 and antibody binding, suggesting that this amino acid contributes to the tertiary structure of CD81 and its ligand-binding ability. These observations have implications for the design of soluble high-affinity molecules that could target the CD81-E2 interaction site(s).

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AplA, a Member of a New Class of Phycobiliproteins Lacking a Traditional Role in Photosynthetic Light Harvesting

Journal of Bacteriology ◽

10.1128/jb.186.21.7420-7428.2004 ◽

2004 ◽

Vol 186 (21) ◽

pp. 7420-7428 ◽

Cited By ~ 13

Author(s):

Beronda L. Montgomery ◽

Elena Silva Casey ◽

Arthur R. Grossman ◽

David M. Kehoe

Keyword(s):

Amino Acid ◽

Tertiary Structure ◽

Light Harvesting ◽

Water Soluble ◽

Amino Acid Residues ◽

Subunit Interactions ◽

Traditional Role ◽

Light Harvesting Complexes ◽

Fremyella Diplosiphon ◽

New Class

ABSTRACT All known phycobiliproteins have light-harvesting roles during photosynthesis and are found in water-soluble phycobilisomes, the light-harvesting complexes of cyanobacteria, cyanelles, and red algae. Phycobiliproteins are chromophore-bearing proteins that exist as heterodimers of α and β subunits, possess a number of highly conserved amino acid residues important for dimerization and chromophore binding, and are invariably 160 to 180 amino acids long. A new and unusual group of proteins that is most closely related to the allophycocyanin members of the phycobiliprotein superfamily has been identified. Each of these proteins, which have been named allophycocyanin-like (Apl) proteins, apparently contains a 28-amino-acid extension at its amino terminus relative to allophycocyanins. Apl family members possess the residues critical for chromophore interactions, but substitutions are present at positions implicated in maintaining the proper α-β subunit interactions and tertiary structure of phycobiliproteins, suggesting that Apl proteins are able to bind chromophores but fail to adopt typical allophycocyanin conformations. AplA isolated from the cyanobacterium Fremyella diplosiphon contained a covalently attached chromophore and, although present in the cell under a number of conditions, was not detected in phycobilisomes. Thus, Apl proteins are a new class of photoreceptors with a different cellular location and structure than any previously described members of the phycobiliprotein superfamily.

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A Rubber-Like Protein in Insect Cuticle

Journal of Experimental Biology ◽

10.1242/jeb.37.4.889 ◽

1960 ◽

Vol 37 (4) ◽

pp. 889-907 ◽

Cited By ~ 17

Author(s):

TORKEL WEIS-FOGH

Keyword(s):

Amino Acid ◽

Tertiary Structure ◽

Three Dimensional ◽

Water Soluble ◽

Insect Cuticle ◽

Peptide Backbone ◽

Experimental Proof ◽

Dimensional Network ◽

New Type ◽

Elastic Protein

1. A new type of hyaline, colourless cuticle, called rubber-like cuticle, is described and analysed qualitatively with respect to mechanical behaviour, structure and composition. Externally it is covered by ordinary thin epicuticle, but otherwise it represents the simplest type of cuticle known and consists only of thin continuous lamellae of chitin (0-2 µ) separated and glued together by an elastic protein, resilin, not hitherto described. There are only traces of water-soluble substances present and resilin sometimes occurs as pure, hyaline patches more than 100 µ thick and suitable for macroscopic experiments. 2. In all physical respects, resilin behaves like a swollen isotropic rubber but the rigid experimental proof is given elsewhere (Weis-Fogh, 1961). An outstanding feature is the complete lack of flow not paralleled by other natural or synthetic rubbers. 3. Resilin resembles elastin but it is devoid of colour and has a different and characteristic amino-acid composition (Bailey & Weis-Fogh, 1961). The nature of the cross-linkages is unknown at present but they are extremely stable, of a co-valent type and different from other known cross-linkages in proteins. This accounts for its insolubility and resistance to all agents which do not break the peptide backbone. 4. Resilin is a structure protein in which the primary chains show little or no tendency to form secondary structures; they are bound together in a uniform three-dimensional network (the tertiary structure) with no potential limits as to size.

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Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat

PLoS ONE ◽

10.1371/journal.pone.0257392 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257392

Author(s):

Muhammad Numan ◽

Shazia Anwer Bukhari ◽

Mahmood-ur- Rehman ◽

Ghulam Mustafa ◽

Bushra Sadia

Keyword(s):

Molecular Docking ◽

Amino Acid ◽

Plant Defense ◽

Fungal Pathogens ◽

Tertiary Structure ◽

Wheat Variety ◽

Wheat Crop ◽

Amino Acid Residues ◽

Beta Glucan ◽

Pathogenesis Related

Wheat is a major staple food and has been extensively grown around the globe. Sessile nature of plants has exposed them to a lot of biotic and abiotic stresses including fungal pathogen attack. Puccinia graminis f.sp. tritici causes stem rust in the wheat crop and leads to 70% decrease in its production. Pathogenesis-related (PR) proteins provide plants with defense against different fungal pathogens as these proteins have antifungal activities. This study was designed to screen Pakistani wheat varieties for PR2 and PR3 proteins and their in silico characterization. PR2 and PR3 genes were screened and isolated by PCR amplification from wheat variety Chenab-70 and Frontana, respectively. The nucleotide sequences of PR2 and PR3 genes were deposited in GenBank with accession numbers MT303867 and MZ766118, respectively. Physicochemical properties, secondary and tertiary structure predictions, and molecular docking of protein sequences of PR2 and PR3 were performed using different bioinformatics tools and software. PR2 and PR3 genes were identified to encode β–1,3–glucanase and chitinase proteins, respectively. Molecular docking of both PR2 and PR3 proteins with beta-glucan and chitin (i.e. their respective ligands) showed crucial amino acid residues involved in molecular interactions. Conclusively, molecular docking analysis of β–1,3–glucanase and chitinase proteins revealed crucial amino acid residues which are involved in ligand binding and important interactions which might have important role in plant defense against fungal pathogens. Moreover, the active residues in the active sties of these proteins can be identified through mutational studies and resulting information might help understanding how these proteins are involved in plant defense mechanisms.

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PROTEIN TERTIARY STRUCTURE PREDICTION BASED ON MAIN CHAIN ANGLE USING A HYBRID BEES COLONY OPTIMIZATION ALGORITHM

International Journal of Modern Physics Conference Series ◽

10.1142/s201019451200520x ◽

2012 ◽

Vol 09 ◽

pp. 143-156 ◽

Cited By ~ 4

Author(s):

ZAKARIA N. MAHMOOD ◽

MASSUDI MAHMUDDIN ◽

MOHAMMED NOORALDEEN MAHMOOD

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Optimization Algorithm ◽

Structure Prediction ◽

Tertiary Structure ◽

Promising Result ◽

3D Structure ◽

Research Area ◽

Prototype System ◽

Protein Tertiary Structure

Encoding proteins of amino acid sequence to predict classified into their respective families and subfamilies is important research area. However for a given protein, knowing the exact action whether hormonal, enzymatic, transmembranal or nuclear receptors does not depend solely on amino acid sequence but on the way the amino acid thread folds as well. This study provides a prototype system that able to predict a protein tertiary structure. Several methods are used to develop and evaluate the system to produce better accuracy in protein 3D structure prediction. The Bees Optimization algorithm which inspired from the honey bees food foraging method, is used in the searching phase. In this study, the experiment is conducted on short sequence proteins that have been used by the previous researches using well-known tools. The proposed approach shows a promising result.

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Crystal structure of rat transthyretin at 2.5 A resolution: first report on a unique tetrameric structure.

Acta Biochimica Polonica ◽

10.18388/abp.1997_4400 ◽

1997 ◽

Vol 44 (3) ◽

pp. 505-517 ◽

Cited By ~ 27

Author(s):

A Wojtczak

Keyword(s):

Amino Acid ◽

Conformational Changes ◽

Tertiary Structure ◽

Amino Acid Residues ◽

Flexible Loop ◽

Tetrameric Structure ◽

Data Points ◽

Loop Regions ◽

Polypeptide Chains ◽

Starting Model

The first observation of a unique tetrameric molecular structure of transthyretin from rat (rTTR, prealbumin) is reported. The structure has been determined by X-ray diffraction using molecular replacement and the structure of human transthyretin (hTTR) as a starting model. Crystals of native rat transthyretin are tetragonal, space group P4(3)2(1)2, and have four independent monomers in the asymmetric unit of the crystal lattice. Data were collected to 2.5 A resolution and the structure has been refined to R = 18.9% for 13584 data points between 8-2.5 A resolution. Like hTTR, the rat protein is also a 54000 Da tetramer with four identical polypeptide chains of 127 amino-acid residues. Of the 22 amino-acid residues which are different in the human and rat TTR sequences, none are in the thyroxine binding domain. Analysis of these data reveal that the tertiary structure of rTTR is similar to that of hTTR with only small differences in the flexible loop regions on the surface of the protein. As a result of local changes in flexible loop regions near residues 30-41, 60-65 and 102-104, the structure of rTTR monomers is more compact than that of the corresponding hTTR monomers. The loop between residues 30-41 is bound closer to the monomer core in the former as compared with the latter structure and there is a wider opening of the space formed between these loops at two adjacent monomeric subunits. These conformational changes do not affect the interfaces between the monomeric subunits and are not transmitted to the thyroxine binding site so that its topology remains not altered.

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