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

1997 ◽  
Vol 44 (3) ◽  
pp. 505-517 ◽  
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.

Evolutionary divergence and salinity-mediated selection in halophilic archaea

1997 ◽  
Vol 61 (1) ◽  
pp. 90-104
Author(s):  
P P Dennis ◽  
L C Shimmin
Keyword(s):  
Amino Acid ◽  
Tertiary Structure ◽  
Halophilic Archaea ◽  
Amino Acid Replacement ◽  
Evolutionary Divergence ◽  
Ionic Balance ◽  
Amino Acid Residues ◽  
Nucleotide Substitutions ◽  
Nonsynonymous Substitutions ◽  
Environmental Salinity

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.

scholarly journals Efficient Subgroup C Avian Sarcoma and Leukosis Virus Receptor Activity Requires the IgV Domain of the Tvc Receptor and Proper Display on the Cell Membrane

2008 ◽  
Vol 82 (22) ◽  
pp. 11419-11428 ◽  
Author(s):  
Audelia Munguia ◽  
Mark J. Federspiel
Keyword(s):  
Amino Acid ◽  
Cell Membrane ◽  
Conformational Changes ◽  
Aromatic Amino Acid ◽  
Receptor Activity ◽  
Site Directed Mutagenesis ◽  
Receptor Interaction ◽  
Common Mechanism ◽  
Amino Acid Residues ◽  
Avian Sarcoma

ABSTRACT We recently identified and cloned the receptor for subgroup C avian sarcoma and leukosis viruses [ASLV(C)], i.e., Tvc, a protein most closely related to mammalian butyrophilins, which are members of the immunoglobulin protein family. The extracellular domain of Tvc contains two immunoglobulin-like domains, IgV and IgC, which presumably each contain a disulfide bond important for native function of the protein. In this study, we have begun to identify the functional determinants of Tvc responsible for ASLV(C) receptor activity. We found that the IgV domain of the Tvc receptor is responsible for interacting with the glycoprotein of ASLV(C). Additional experiments demonstrated that a domain was necessary as a spacer between the IgV domain and the membrane-spanning domain for efficient Tvc receptor activity, most likely to orient the IgV domain a proper distance from the cell membrane. The effects on ASLV(C) glycoprotein binding and infection efficiency were also studied by site-directed mutagenesis of the cysteine residues of Tvc as well as conserved amino acid residues of the IgV Tvc domain compared to other IgV domains. In this initial analysis of Tvc determinants important for interacting with ASLV(C) glycoproteins, at least two aromatic amino acid residues in the IgV domain of Tvc, Trp-48 and Tyr-105, were identified as critical for efficient ASLV(C) infection. Interestingly, one or more aromatic amino acid residues have been identified as critical determinants in the other ASLV(A-E) receptors for a proper interaction with ASLV glycoproteins. This suggests that the ASLV glycoproteins may share a common mechanism of receptor interaction with an aromatic residue(s) on the receptor critical for triggering conformational changes in SU that initiate the fusion process required for efficient virus infection.

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

2000 ◽  
Vol 74 (8) ◽  
pp. 3642-3649 ◽  
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).

scholarly journals Amino acid sequences around the cysteine residues of rabbit muscle triose phosphate isomerase

1971 ◽  
Vol 122 (2) ◽  
pp. 209-218 ◽  
Author(s):  
Janet C. Miller ◽  
S. G. Waley
Keyword(s):  
Amino Acid ◽  
Cyanogen Bromide ◽  
Triose Phosphate Isomerase ◽  
Amino Acid Sequences ◽  
Cysteine Residues ◽  
Rabbit Muscle ◽  
Amino Acid Residues ◽  
Triose Phosphate ◽  
Methionine Residues ◽  
Polypeptide Chains

1. The nature of the subunits in rabbit muscle triose phosphate isomerase has been investigated. 2. Amino acid analyses show that there are five cysteine residues and two methionine residues/subunit. 3. The amino acid sequences around the cysteine residues have been determined; these account for about 75 residues. 4. Cleavage at the methionine residues with cyanogen bromide gave three fragments. 5. These results show that the subunits correspond to polypeptide chains, containing about 230 amino acid residues. The chains in triose phosphate isomerase seem to be shorter than those of other glycolytic enzymes.

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

2004 ◽  
Vol 186 (21) ◽  
pp. 7420-7428 ◽  
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.

scholarly journals Localization of Ca2+-dependent conformational changes of calretinin by limited tryptic proteolysis

1995 ◽  
Vol 308 (2) ◽  
pp. 607-612 ◽  
Author(s):  
J Kuźnicki ◽  
T L Wang ◽  
B M Martin ◽  
L Winsky ◽  
D M Jacobowitz
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Conformational Changes ◽  
Cleavage Sites ◽  
Amino Acid Residues ◽  
Amino Acid Sequence Analysis ◽  
Sds Page ◽  
Ef Hand ◽  
Digestion Pattern

Calretinin is an EF-hand Ca(2+)-binding protein expressed predominantly in some neurons. We have found that the tryptic digestion pattern of rat recombinant calretinin depends on Ca2+ concentration as determined by SDS/PAGE, amino-acid-sequence analysis and electrospray-ionization MS. Ca(2+)-saturated calretinin was cleaved between amino acids 60 and 61 to yield two fragments, which accumulated during cleavage. Small amounts of the larger fragment (amino acid residues 61-271) were further cleaved from the C-terminal end. Ca(2+)-free calretinin was also cleaved between residues 60 and 61; however, under the latter conditions the fragment 61-271 was further cleaved from the N-terminal end. Native rat calretinin was cleaved by trypsin in a similar Ca(2+)-dependent fashion. All identified fragments of recombinant calretinin bound 45Ca2+ on nitrocellulose filters, although to a different extent. The 61-271 fragment was released by EGTA from an octyl-agarose column in a manner similar to intact calretinin, while fragment 61-233 was not eluted by EGTA. These observations show that there are trypsin cleavage sites in calretinin that are available regardless of Ca2+ binding, other sites that are completely protected against trypsin on Ca(2+)-binding and sites which become partially available on Ca(2+)-binding. Together these data show that calretinin changes its conformation on Ca2+ binding and identify the regions which are exposed in apo and Ca(2+)-bound form.

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

PLoS ONE ◽  
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.

scholarly journals Analysis of Binding Sites for the New Small-Molecule CCR5 Antagonist TAK-220 on Human CCR5

2005 ◽  
Vol 49 (11) ◽  
pp. 4708-4715 ◽  
Author(s):  
Masao Nishikawa ◽  
Katsunori Takashima ◽  
Toshiya Nishi ◽  
Rika A. Furuta ◽  
Naoyuki Kanzaki ◽  
...  
Keyword(s):  
Amino Acid ◽  
Small Molecule ◽  
Conformational Changes ◽  
Binding Pocket ◽  
Inhibitory Effect ◽  
Ccr5 Antagonist ◽  
Amino Acid Residues ◽  
Ccr5 Antagonists ◽  
Human Ccr5 ◽  
Hiv 1

ABSTRACT G protein-coupled receptor CCR5 is the main coreceptor for macrophage-tropic human immunodeficiency virus type 1 (HIV-1), and various small-molecule CCR5 antagonists are being developed to treat HIV-1 infection. It has been reported that such CCR5 antagonists, including TAK-779, bind to a putative binding pocket formed by transmembrane domains (TMs) 1, 2, 3 and 7 of CCR5, indicating the importance of the conformational changes of the TMs during virus entry. In this report, using a single-round infection assay with human CCR5 and its substitution mutants, we demonstrated that a new CCR5 antagonist, TAK-220, shares the putative interacting amino acid residues Asn252 and Leu255 in TM6 with TAK-779 but also requires the distinct residues Gly163 and Ile198 in TMs 4 and 5, respectively, for its inhibitory effect. We suggested that, together with molecular models of the interactions between the drugs and CCR5, the inhibitory activity of TAK-220 could involve direct interactions with amino acid residues in TMs 4, 5, and 6 in addition to those in the previously postulated binding pocket. The possible interaction of drugs with additional regions of the CCR5 molecule would help to develop a new small-molecule CCR5 antagonist.

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