A cluster of diagnostic Hsp68 amino acid sites that are identified in Drosophila from the melanogaster species group are concentrated around β-sheet residues involved with substrate binding

Genome ◽  
2005 ◽  
Vol 48 (2) ◽  
pp. 226-233 ◽  
Author(s):  
Mark Kellett ◽  
Stephen W McKechnie
Keyword(s):  
Amino Acid ◽  
Substrate Binding ◽  
Acid Sites ◽  
Amino Acid Sequences ◽  
Length Variation ◽  
Functional Sites ◽  
Structure Conservation ◽  
Α Helix ◽  
Montium Subgroup ◽  
Β Sheet

The coding region of the hsp68 gene has been amplified, cloned, and sequenced from 10 Drosophila species, 5 from the melanogaster subgroup and 5 from the montium subgroup. When the predicted amino acid sequences are compared with available Hsp70 sequences, patterns of conservation suggest that the C-terminal region should be subdivided according to predominant secondary structure. Conservation levels between Hsp68 and Hsp70 proteins were high in the N-terminal ATPase and adjacent β-sheet domains, medium in the α-helix domain, and low in the C-terminal mobile domain (78%, 72%, 41%, and 21% identity, respectively). A number of amino acid sites were found to be "diagnostic" for Hsp68 (28 of ~635 residues). A few of these occur in the ATPase domain (385 residues) but most (75%) are concentrated in the β-sheet and α-helix domains (34% of the protein) with none in the short mobile domain. Five of the diagnostic sites in the β-sheet domain are clustered around, but not coincident with, functional sites known to be involved in substrate binding. Nearly all of the Hsp70 family length variation occurs in the mobile domain. Within montium subgroup species, 2 nearly identical hsp68 PCR products that differed in length are either different alleles or products of an ancestral hsp68 duplication.Key words: Hsp70, Hsp68, diagnostic sites, Drosophila melanogaster, montium subgroup.

Relation Of Heparin Binding And Conformation In PF4 AND LA-PF4 (βTG)

1981 ◽  
Author(s):  
John C Holt ◽  
Marek Kloczewiak ◽  
Daniel A Walz ◽  
Boguslaw Rucinski ◽  
Stefan Niewiarowski
Keyword(s):  
Amino Acid ◽  
Disulfide Bonds ◽  
Amino Acid Sequences ◽  
Platelet Factor 4 ◽  
Heparin Binding ◽  
Platelet Factor ◽  
Significant Difference ◽  
Lysine Residues ◽  
Α Helix ◽  
Β Sheet

Platelet factor 4 (PF4) and low affinity platelet factor 4 (LA-PF4) are platelet-specific secreted proteins that bind to heparin. β-thromboglobulin (βTG) appears to be derived from LA-PF4 by proteolysis of four NH2-terminal residues. PF4 and LA-PF4 (βTG) show 50% sequence homology including four cysteine residues and two pairs of lysine residues near the C00H-terminus which are believed to be responsible for heparin binding. Despite these similarities, the two proteins have markedly different affinities for heparin. We have sought a structural interpretation of this difference by predicting the conformations of 0TG, LA-PF4 and PF4. First, the proportion of residues in α-helical, β-sheet and unordered conformations was estimated from circular dichroism measurements. The results for PF4 and LA-PF4 were experimentally identical, namely 16% α-helix and 20% β-sheet. These values were then applied as experimental constraints in the prediction of the secondary structure of PF4 and LA-PF4 based on their amino acid sequences. This was done by a computer program which compared local amino acid sequence (each residue and 8 residues on either side) with the conformation of similar sequences in 25 proteins of known structure. With the further constraint of the two disulfide bonds in each molecule, models were constructed representing the overall folding of the polypeptide chains. The only significant difference between the two proteins was in the COOH-terminal region of the chains. The models suggest that the lower affinity of LA-PF4 (and βTG) for heparin may result from steric hindrance by the longer and more negatively charged COOH-terminal segments of these molecules compared with PF4.

scholarly journals Insights into the Selective Pressures Restricting Pelargonium Flower Break Virus Genome Variability: Evidence for Host Adaptation

2006 ◽  
Vol 80 (16) ◽  
pp. 8124-8132 ◽  
Author(s):  
Patricia Rico ◽  
Pilar Ivars ◽  
Santiago F. Elena ◽  
Carmen Hernández
Keyword(s):  
Amino Acid ◽  
Leucine Zipper ◽  
Critical Role ◽  
Chenopodium Quinoa ◽  
Virus Genome ◽  
Acid Sites ◽  
Genomic Region ◽  
Amino Acid Sequences ◽  
Nucleotide Substitutions ◽  
Selective Pressures

ABSTRACT The molecular diversity of Pelargonium flower break virus (PFBV) was assessed using a collection of isolates from different geographical origins, hosts, and collecting times. The genomic region examined was 1,828 nucleotides (nt) long and comprised the coding sequences for the movement (p7 and p12) and the coat (CP) proteins, as well as flanking segments including the entire 3′ untranslated region (3′ UTR). Some constraints limiting viral heterogeneity could be inferred from sequence analyses, such as the conservation of the amino acid sequences of p7 and of the shell domain of the CP, the maintenance of a leucine zipper motif in p12, and the preservation of a particular folding in the 3′ UTR. A remarkable covariation, involving five specific amino acid sites, was found in the CP of isolates largely propagated in the local lesion host Chenopodium quinoa and in the progeny of a PFBV variant subjected to serial passages in this host. Concomitant with this covariation, up to 30 nucleotide substitutions in a 1,428-nt region of the viral RNA could be attributable to C. quinoa-specific adaptation, representing one of the most outstanding cases of host-driven genome variation for a plant virus. Globally, the results indicate that the selective pressures exerted by the host play a critical role in shaping PFBV populations and that these populations are likely being selected for at both protein and RNA levels.

scholarly journals Structural and Physical Properties of a Necrosis-Inducing Toxin from Pyrenophora tritici-repentis

1997 ◽  
Vol 87 (2) ◽  
pp. 154-160 ◽  
Author(s):  
Hui-Fen Zhang ◽  
Leonard J. Francl ◽  
James G. Jordahl ◽  
Steven W. Meinhardt
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Cd Spectroscopy ◽  
Tan Spot ◽  
Pyrenophora Tritici Repentis ◽  
Membrane Adhesion ◽  
Α Helix ◽  
Β Sheet

Cultivar-specific toxic metabolites of Pyrenophora tritici-repentis are involved in the appearance of necrotic and chlorotic foliar lesions characteristic of tan spot. A P. tritici-repentis necrosis-inducing toxin, Ptr necrosis toxin, was purified from isolate 86-124, sequenced by gas-phase amino acid microsequencing, and characterized by circular dichroism (CD) spectroscopy and isoelectric focusing. The purified protein had a similar amino acid composition and molecular weight as previously reported. Analysis of the CD spectrum from 178 to 250 nm indicated a protein consisting of 13% α-helix, 36% antiparallel β-sheet, 25% turns, and 25% other structures. The Ptr necrosis toxin from isolate 86-124 has an isoelectric point near pH 10. Using overlapping proteolytic fragments obtained from the toxin, a sequence of 101 continuous amino acids was obtained, but the amino terminus was blocked and 9 to 16 amino acids could not be sequenced. Secondary structure prediction based on the amino acid sequence indicated a β-sheet protein with little α-helix, which is in agreement with the structure determined by CD spectroscopy. Sequence analysis indicated the presence of a possible membrane adhesion site and several possible phosphorylation sites that may be involved in phytotoxicity.

scholarly journals Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10017
Author(s):  
Raden Pramesa Narakusumo ◽  
Alexander Riedel ◽  
Joan Pons
Keyword(s):  
Amino Acid ◽  
Phylogenetic Signal ◽  
Mitochondrial Protein ◽  
Amino Acid Sequences ◽  
Mitochondrial Genomes ◽  
Length Variation ◽  
Codon Site ◽  
Protein Coding ◽  
Large Variability ◽  
Molecular Features

Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.

What vibrations tell about proteins

2002 ◽  
Vol 35 (4) ◽  
pp. 369-430 ◽  
Author(s):  
Andreas Barth ◽  
Christian Zscherp
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Ir Spectroscopy ◽  
Reaction Mechanisms ◽  
Amino Acid Side Chain ◽  
Difference Spectroscopy ◽  
Transition Dipole ◽  
Dipole Coupling ◽  
Α Helix ◽  
Β Sheet

1. Introduction 3702. Infrared (IR) spectroscopy – general principles 3722.1 Vibrations 3722.2 Information that can be derived from the vibrational spectrum 3722.3 Absorption of IR light 3753. Protein IR absorption 3763.1 Amino-acid side-chain absorption 3763.2 Normal modes of the amide group 3814. Interactions that shape the amide I band 3824.1 Overview 3824.2 Through-bond coupling 3834.3 Hydrogen bonding 3834.4 Transition dipole coupling (TDC) 3835. The polarization and IR activity of amide I modes 3875.1 The coupled oscillator system 3875.2 Optically allowed transitions 3885.3 The infinite parallel β-sheet 3885.4 The infinite antiparallel β-sheet 3895.5 The infinite α-helix 3906. Calculation of the amide I band 3916.1 Overview 3916.2 Perturbation treatment by Miyazawa 3936.3 The parallel β-sheet 3946.4 The antiparallel β-sheet 3956.5 The α-helix 3966.6 Other secondary structures 3987. Experimental analysis of protein secondary structure 3987.1 Band fitting 3987.2 Methods using calibration sets 4017.3 Prediction quality 4038. Protein stability 4048.1 Thermal stability 4048.2 1H/2H exchange 4069. Molecular reaction mechanisms of proteins 4089.1 Reaction-induced IR difference spectroscopy 4089.2 The origin of difference bands 4099.3 The difference spectrum seen as a fingerprint of conformational change 4109.4 Molecular interpretation: strategies of band assignment 41610. Outlook 41911. Acknowledgements 42012. References 420This review deals with current concepts of vibrational spectroscopy for the investigation of protein structure and function. While the focus is on infrared (IR) spectroscopy, some of the general aspects also apply to Raman spectroscopy. Special emphasis is on the amide I vibration of the polypeptide backbone that is used for secondary-structure analysis. Theoretical as well as experimental aspects are covered including transition dipole coupling. Further topics are discussed, namely the absorption of amino-acid side-chains, 1H/2H exchange to study the conformational flexibility and reaction-induced difference spectroscopy for the investigation of reaction mechanisms with a focus on interpretation tools.

scholarly journals Sequence analysis and structure prediction of ABHD16A and the roles of the ABHD family members in human disease

Open Biology ◽  
2018 ◽  
Vol 8 (5) ◽  
pp. 180017 ◽  
Author(s):  
Jun Xu ◽  
Weizhen Gu ◽  
Kai Ji ◽  
Zhao Xu ◽  
Haihua Zhu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Active Sites ◽  
Metabolic Regulation ◽  
Acid Sites ◽  
Amino Acid Sequences ◽  
The Body ◽  
Gene Location ◽  
Future Research ◽  
Animal Cells

Abhydrolase domain containing 16A (ABHD16A) is a member of the α/β hydrolase domain-containing (ABHD) protein family and is expressed in a variety of animal cells. Studies have shown that ABHD16A has acylglycerol lipase and phosphatidylserine lipase activities. Its gene location in the main histocompatibility complex (MHC) III gene cluster suggests that this protein may participate in the immunomodulation of the body. The results of studies investigating nearly 20 species of ABHDs reveal that the ABHD proteins are key factors in metabolic regulation and disease occurrence and development. In this paper, we summarize the related progress regarding the function of ABHD16A and other ABHD proteins. A prediction of the active sites and structural domains of ABHD16A and an analysis of the amino acid sites are included. Moreover, we analysed the amino acid sequences of the ABHD16A molecules in different species and provide an overview of the related functions and diseases associated with these proteins. The functions and diseases related to ABHD are systematically summarized and highlighted. Future research directions for studies investigating the functions and mechanisms of these proteins are also suggested. Further studies investigating the function of ABHD proteins may further confirm their positions as important determinants of lipid metabolism and related diseases.

scholarly journals Mutagenesis of Critical Amino Acid Residues in α-Helix and β-Sheet Structures of Brazzein

2011 ◽  
Vol 32 (11) ◽  
pp. 4106-4108 ◽  
Author(s):  
Hyun-Dong Do ◽  
Hyun-Joo Jo ◽  
Dong-Hyeon Jo ◽  
Kwang-Hoon Kong
Keyword(s):  
Amino Acid ◽  
Amino Acid Residues ◽  
Critical Amino Acid ◽  
Α Helix ◽  
Β Sheet

Cloning and Characterization of Three Genes Encoding LMW-GSs from Triticum aestivum, Cultival Cheyenne

2012 ◽  
Vol 554-556 ◽  
pp. 1116-1120 ◽  
Author(s):  
Mei Rong Chen ◽  
Xing Shen ◽  
Lin Li ◽  
Song Qing Hu
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Amino Acid Residues ◽  
Repetitive Domain ◽  
Genebank Accession ◽  
Genes Encoding ◽  
Α Helix ◽  
Β Sheet

Three low molecular weight subunit genes, named LMW-CND1 (GeneBank accession JQ780048), LMW-CND2 (GeneBank accession JQ779840), LMW-CND3 (GeneBank accession JQ779841), with a ORF of 1053 bp, 903 bp, 969 bp, respectively, were isolated from cv. Cheyenne and characterized detailed in molecular level. The proteins encoded by the genes, with 350, 300, 322 amino acid residues respectively, differ only in repetitive domain of sequences due to insertion or deletion of repeats in this domain. Highly similarity in amino-acid sequence between these three subunits and other published LMW-GSs was also observed, showing that all three genes published here are typical LMW-GS genes and closely related to the genes on chromosome 1D. Besides, secondary structure prediction of proteins indicated that, in the three LMW-GSs, random loop accounts for no less than 70 %, α-helix amounts to 26 %, average, and only 1.4 %~1.7 % is β-sheet.

scholarly journals New fungal defensin-like peptides provide evidence for fold change of proteins in evolution

2017 ◽  
Vol 37 (1) ◽  
Author(s):  
Yucheng Wu ◽  
Bin Gao ◽  
Shunyi Zhu
Keyword(s):  
Disulfide Bridge ◽  
Fold Change ◽  
Structure Conservation ◽  
Fold Formation ◽  
Fungal Defensin ◽  
Α Helix ◽  
Residue Numbers ◽  
Evolution Of Proteins ◽  
Multicellular Organisms ◽  
Β Sheet

Defensins containing a consensus cystine framework, Cys[1]…Cys[2]X3Cys[3]…Cys[4]… Cys[5]X1Cys[6] (X, any amino acid except Cys; …, variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming the cysteine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys[2]X3Cys[3]/Cys[5]X1Cys[6], are key determinants of fold formation. By using a computational genomics approach, we identified a large superfamily of fungal defensin-like peptides (fDLPs) in the phytopathogenic fungal genus – Zymoseptoria, which includes 132 structurally typical and 63 atypical members. These atypical fDLPs exhibit an altered cystine framework and accompanying fold change associated with their secondary structure elements and disulfide bridge patterns, as identified by protein structure modelling. Despite this, they definitely are homologous with the typical fDLPs in view of their precise gene structure conservation and identical precursor organization. Sequence and structural analyses combined with functional data suggest that most of Zymoseptoria fDLPs might have lost their antimicrobial activity. The present study provides a clear example of fold change in the evolution of proteins and is valuable in establishing remote homology among peptide superfamily members with different folds.

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