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 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 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 Inferring amino acid interactions underlying protein function

2017 ◽  
Author(s):  
Victor H. Salinas ◽  
Rama Ranganathan
Keyword(s):  
Amino Acid ◽  
Protein Function ◽  
Structural Basis ◽  
Evolutionary Divergence ◽  
Amino Acid Residues ◽  
Homologous Proteins ◽  
Physical Constraints ◽  
Spatially Distributed ◽  
Statistical Coupling ◽  
Energetic Interactions

Protein function arises from a poorly defined pattern of cooperative energetic interactions between amino acid residues. Strategies for deducing this pattern have been proposed, but lack of benchmark data has limited experimental verification. Here, we extend deep-mutation technologies to enable measurement of many thousands of pairwise amino acid couplings in members of a protein family. The data show that despite great evolutionary divergence, homologous proteins conserve a sparse, spatially distributed network of cooperative interactions between amino acids that underlies function. This pattern is quantitatively captured in the coevolution of amino acid positions, especially as indicated by the statistical coupling analysis (SCA), providing experimental confirmation of the key tenets of this method. This work establishes a clear link between physical constraints on protein function and sequence analysis, enabling a general practical approach for understanding the structural basis for protein function.

scholarly journals Characterisation andIn SilicoAnalysis of Interleukin-4 cDNA of Nilgai (Boselaphus tragocamelus) and Indian Buffalo (Bubalus bubalis)

2013 ◽  
Vol 2013 ◽  
pp. 1-7
Author(s):  
M. Saini ◽  
T. K. Palai ◽  
D. K. Das ◽  
K. M. Hatle ◽  
P. K. Gupta
Keyword(s):  
Amino Acid ◽  
Mononuclear Cells ◽  
Tertiary Structure ◽  
Interleukin 4 ◽  
Laboratory Animals ◽  
Th2 Cells ◽  
Common Belief ◽  
Wild Animals ◽  
Nucleotide Substitutions ◽  
Peripheral Blood Mononuclear

Interleukin-4 (IL-4) produced from Th2 cells modulates both innate and adaptive immune responses. It is a common belief that wild animals possess better immunity against diseases than domestic and laboratory animals; however, the immune system of wild animals is not fully explored yet. Therefore, a comparative study was designed to explore the wildlife immunity through characterisation of IL-4 cDNA of nilgai, a wild ruminant, and Indian buffalo, a domestic ruminant. Total RNA was extracted from peripheral blood mononuclear cells of nilgai and Indian buffalo and reverse transcribed into cDNA. Respective cDNA was further cloned and sequenced. Sequences were analysed in silico and compared with their homologues available at GenBank. The deduced 135 amino acid protein of nilgai IL-4 is 95.6% similar to that of Indian buffalo. N-linked glycosylation sequence, leader sequence, Cysteine residues in the signal peptide region, and 3′ UTR of IL-4 were found to be conserved across species. Six nonsynonymous nucleotide substitutions were found in Indian buffalo compared to nilgai amino acid sequence. Tertiary structure of this protein in both species was modeled, and it was found that this protein falls under 4-helical cytokines superfamily and short chain cytokine family. Phylogenetic analysis revealed a single cluster of ruminants including both nilgai and Indian buffalo that was placed distinct from other nonruminant mammals.

scholarly journals Structural requirement of the calcium-channel subunit α2δ for gabapentin binding

1999 ◽  
Vol 342 (2) ◽  
pp. 313-320 ◽  
Author(s):  
Minghan WANG ◽  
James OFFORD ◽  
Dale L. OXENDER ◽  
Ti-Zhi SU
Keyword(s):  
Amino Acid ◽  
Structural Integrity ◽  
Transmembrane Domain ◽  
Anticonvulsant Drug ◽  
Amino Acid Replacement ◽  
Significant Loss ◽  
Single Amino Acid ◽  
Amino Acid Residues ◽  
Structural Requirement ◽  
High Binding Affinity

Gabapentin [Neurontin, 1-(aminomethyl)cyclohexaneacetic acid] is a novel anticonvulsant drug with a high binding affinity for the Ca2+-channel subunit α2δ. In this study, the gabapentin-binding properties of wild-type and mutated porcine brain α2δ proteins were investigated. Removal of the disulphide bonds between the α2 and the δ subunits did not result in a significant loss of gabapentin binding, suggesting that the disulphide linkage between the two subunits is not required for binding. Singly expressed α2 protein remained membrane associated. However, α2 alone was unable to bind gabapentin, unless the cells were concurrently transfected with the expression vector for δ, suggesting that both α2 and δ are required for gabapentin binding. Using internal deletion mutagenesis, we mapped two regions [amino acid residues 339-365 (δF) and 875-905 (δJ)] within the α2 subunit that are not required for gabapentin binding. Further, deletion of three other individual regions [amino acid residues 206-222 (δD), 516-537 (δH) and 583-603 (δI)] within the α2 subunit disrupted gabapentin binding, suggesting the structural importance of these regions. Using alanine to replace four to six amino acid residues in each of these regions abolished gabapentin binding. These results demonstrate that region D, between the N-terminal end and the first putative transmembrane domain of α2, and regions H and I, between the putative splicing acceptor sites (Gln511 and Ser601), may play important roles in maintaining the structural integrity for gabapentin binding. Further single amino acid replacement mutagenesis within these regions identified Arg217 as critical for gabapentin binding.

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 Characterization of the Enzymatic Component of Clostridium perfringens Iota-Toxin

2000 ◽  
Vol 182 (8) ◽  
pp. 2096-2103 ◽  
Author(s):  
Masahiro Nagahama ◽  
Yoshihiko Sakaguchi ◽  
Keiko Kobayashi ◽  
Sadayuki Ochi ◽  
Jun Sakurai
Keyword(s):  
Amino Acid ◽  
Aspartic Acid ◽  
Clostridium Perfringens ◽  
Amino Acid Replacement ◽  
Complete Loss ◽  
Cytotoxic Activities ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Drastic Reduction ◽  
Clostridium Perfringens Iota Toxin

ABSTRACT The iotaa component (ia) ofClostridium perfringens ADP ribosylates nonmuscle β/γ actin and skeletal muscle α-actin. Replacement of Arg-295 in ia with alanine led to a complete loss of NAD+-glycohydrolase (NADase) and ADP-ribosyltransferase (ARTase); that of the residue with lysine caused a drastic reduction in NADase and ARTase activities (<0.1% of the wild-type activities) but did not completely diminish them. Substitution of alanine for Glu-378 and Glu-380 caused a complete loss of NADase and ARTase. However, exchange of Glu-378 to aspartic acid or glutamine resulted in little effect on NADase activity but a drastic reduction in ARTase activity (<0.1% of the wild-type activity). Exchange of Glu-380 to aspartic acid caused a drastic reduction in NADase and ARTase activities (<0.1% of the wild-type activities) but did not completely diminish them; that of the residue to glutamine caused a complete loss of ARTase activity. Replacement of Ser-338 with alanine resulted in 0.7 to 2.3% wild-type activities, and that of Ser-340 and Thr-339 caused a reduction in these activities of 5 to 30% wild-type activities. The kinetic analysis showed that Arg-295 and Ser-338 also play an important role in the binding of NAD+ to ia, that Arg-295, Glu-380, and Ser-338 play a crucial role in the catalytic rate of NADase activity, and that these three amino acid residues and Glu-378 are essential for ARTase activity. The effect of amino acid replacement in ia on ARTase activity was similar to that on lethal and cytotoxic activities, suggesting that lethal and cytotoxic activities in ia are dependent on ARTase activity.

In silico analysis and effects of environmental salinity in the expression and activity of digestive α-amylase and trypsins from the euryhaline crab Neohelice granulata

2018 ◽  
Vol 96 (2) ◽  
pp. 127-139
Author(s):  
Antonela Asaro ◽  
Juan Antonio Martos-Sitcha ◽  
Gonzalo Martínez-Rodríguez ◽  
Juan Miguel Mancera ◽  
Alejandra Antonia López Mañanes
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Amylase Activity ◽  
Mrna Level ◽  
Molecular Characteristics ◽  
Mrna Levels ◽  
Amino Acid Residues ◽  
Salinity Acclimation ◽  
Neohelice Granulata ◽  
Environmental Salinity

Studies on molecular characteristics and modulation of expression of α-amylase and trypsin in the hepatopancreas of intertidal euryhaline crabs are lacking. In this work, we cloned and studied by in silico approaches the characteristics of cDNA sequences for α-amylase and two trypsins isoforms, as well as the effect of environmental salinity, on gene expression and protein activities in the hepatopancreas of Neohelice granulata (Dana, 1851), which is a good invertebrate model species. The cDNA sequence of α-amylase is 1637 bp long, encoding 459 amino acid residues. Trypsin 1 and 2 are 689 and 1174 bp long, encoding 204 and 151 amino acid residues, respectively. Multiple sequence alignment of deduced protein sequences revealed the presence of conserved motifs found in other invertebrates. In crabs acclimated at 37 psu (hyporegulation), α-amylase mRNA level and total pancreatic amylase activity were higher than at 10 psu (hyperregulation) and 35 psu (osmoconformation). Trypsin 1 mRNA levels increased at 37 psu, while trypsin 2 levels decreased at 10 and 37 psu. Total trypsin activity was similar in all salinities. Our results showed a differential modulation of α-amylase and trypsin expression and total amylase activity by salinity acclimation, suggesting the occurrence of distinct mechanisms of regulation at different levels that could lead to digestive adjustments in relation to hyperregulation and (or) hyporegulation.

scholarly journals Substrate Range and Genetic Analysis ofAcinetobacter Vanillate Demethylase

2000 ◽  
Vol 182 (5) ◽  
pp. 1383-1389 ◽  
Author(s):  
Birgit Morawski ◽  
Ana Segura ◽  
L. Nicholas Ornston
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitutions ◽  
Missense Mutations ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Nucleotide Substitutions ◽  
Two Component ◽  
Selection For ◽  
Type Sequence ◽  
Selection Of

ABSTRACT An Acinetobacter sp. genetic screen was used to probe structure-function relationships in vanillate demethylase, a two-component monooxygenase. Mutants with null, leaky, and heat-sensitive phenotypes were isolated. Missense mutations tended to be clustered in specific regions, most of which make known contributions to catalytic activity. The vanillate analogsm-anisate, m-toluate, and 4-hydroxy-3,5-dimethylbenzoate are substrates of the enzyme and weakly inhibit the metabolism of vanillate by wild-typeAcinetobacter bacteria. PCR mutagenesis ofvanAB, followed by selection for strains unable to metabolize vanillate, yielded mutant organisms in which vanillate metabolism is more strongly inhibited by the vanillate analogs. Thus, the procedure opens for investigation amino acid residues that may contribute to the binding of either vanillate or its chemical analogs to wild-type and mutant vanillate demethylases. Selection of phenotypic revertants following PCR mutagenesis gave an indication of the extent to which amino acid substitutions can be tolerated at specified positions. In some cases, only true reversion to the original amino acid was observed. In other examples, a range of amino acid substitutions was tolerated. In one instance, phenotypic reversion failed to produce a protein with the original wild-type sequence. In this example, constraints favoring certain nucleotide substitutions appear to be imposed at the DNA level.

scholarly journals Phylogenetic mixture models for proteins

2008 ◽  
Vol 363 (1512) ◽  
pp. 3965-3976 ◽  
Author(s):  
Si Quang Le ◽  
Nicolas Lartillot ◽  
Olivier Gascuel
Keyword(s):  
Amino Acid ◽  
Mixture Models ◽  
Model Comparison ◽  
Tertiary Structure ◽  
Amino Acid Replacement ◽  
Single Amino Acid ◽  
Learning Approaches ◽  
Solvent Exposure ◽  
Substitution Pattern ◽  
Better Than

Standard protein substitution models use a single amino acid replacement rate matrix that summarizes the biological, chemical and physical properties of amino acids. However, site evolution is highly heterogeneous and depends on many factors: genetic code; solvent exposure; secondary and tertiary structure; protein function; etc. These impact the substitution pattern and, in most cases, a single replacement matrix is not enough to represent all the complexity of the evolutionary processes. This paper explores in maximum-likelihood framework phylogenetic mixture models that combine several amino acid replacement matrices to better fit protein evolution. We learn these mixture models from a large alignment database extracted from HSSP, and test the performance using independent alignments from TreeBase . We compare unsupervised learning approaches, where the site categories are unknown, to supervised ones, where in estimations we use the known category of each site, based on its exposure or its secondary structure. All our models are combined with gamma-distributed rates across sites. Results show that highly significant likelihood gains are obtained when using mixture models compared with the best available single replacement matrices. Mixtures of matrices also improve over mixtures of profiles in the manner of the CAT model. The unsupervised approach tends to be better than the supervised one, but it appears difficult to implement and highly sensitive to the starting values of the parameters, meaning that the supervised approach is still of interest for initialization and model comparison. Using an unsupervised model involving three matrices, the average AIC gain per site with TreeBase test alignments is 0.31, 0.49 and 0.61 compared with LG (named after Le & Gascuel 2008 Mol. Biol. Evol. 25 , 1307–1320), WAG and JTT, respectively. This three-matrix model is significantly better than LG for 34 alignments (among 57), and significantly worse for 1 alignment only. Moreover, tree topologies inferred with our mixture models frequently differ from those obtained with single matrices, indicating that using these mixtures impacts not only the likelihood value but also the output tree. All our models and a PhyML implementation are available from http://atgc.lirmm.fr/mixtures .

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