Prediction of Glycolipid-Binding Domains from the Amino Acid Sequence of Lipid Raft-Associated Proteins:  Application to HpaA, a Protein Involved in the Adhesion ofHelicobacter pylorito Gastrointestinal Cells

Biochemistry ◽  
2006 ◽  
Vol 45 (36) ◽  
pp. 10957-10962 ◽  
Author(s):  
Jacques Fantini ◽  
Nicolas Garmy ◽  
Nouara Yahi
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Lipid Raft ◽  
Binding Domains ◽  
Associated Proteins

Nucleoid-associated proteins in Crenarchaea

2011 ◽  
Vol 39 (1) ◽  
pp. 116-121 ◽  
Author(s):  
Rosalie P.C. Driessen ◽  
Remus Th. Dame
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Structural Effect ◽  
Chromatin Organization ◽  
Large Set ◽  
Chromosomal Dna ◽  
Amino Acid Sequence Level ◽  
Generic Level ◽  
Architectural Proteins ◽  
Associated Proteins

Architectural proteins play an important role in compacting and organizing the chromosomal DNA in all three kingdoms of life (Eukarya, Bacteria and Archaea). These proteins are generally not conserved at the amino acid sequence level, but the mechanisms by which they modulate the genome do seem to be functionally conserved across kingdoms. On a generic level, architectural proteins can be classified based on their structural effect as DNA benders, DNA bridgers or DNA wrappers. Although chromatin organization in archaea has not been studied extensively, quite a number of architectural proteins have been identified. In the present paper, we summarize the knowledge currently available on these proteins in Crenarchaea. By the type of architectural proteins available, the crenarchaeal nucleoid shows similarities with that of Bacteria. It relies on the action of a large set of small, abundant and generally basic proteins to compact and organize their genome and to modulate its activity.

A new member of the troponin C superfamily: Comparison of the primary structures of rat oncomodulin and rat parvalbumin

1983 ◽  
Vol 3 (11) ◽  
pp. 1071-1075 ◽  
Author(s):  
J. P. Mac Manus ◽  
D. C. Watson ◽  
M. Yaguchi
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Isoelectric Point ◽  
Base Pair ◽  
Calcium Binding ◽  
Troponin C ◽  
Calcium Binding Protein ◽  
Single Base ◽  
Binding Domains ◽  
Single Base Pair

When the amino-acid sequence of the 108-residue, rat tumour calcium-binding protein, oncomodulin, was aligned with that of rat muscle parvalbumin, 55 homologous positions were found, with an additional 33 single base-pair substitutions. This extensive homology, with virtual identity of the calcium-binding domains, signalled oncomodulin to be a member of the troponin C superfamily. The presence of Cys-18 and Phe-66 in oncomodulin, plus its isoelectric point of 3.9) suggest that this tumour protein is a 8-parva Jbumin, rather than a muscle α-parvalbumin.

scholarly journals Substrate-binding domains of glycanases from Streptomyces lividans: characterization of a new family of xylan-binding domains

1998 ◽  
Vol 330 (1) ◽  
pp. 41-45 ◽  
Author(s):  
Claude DUPONT ◽  
Martin ROBERGE ◽  
François SHARECK ◽  
Rolf MOROSOLI ◽  
Dieter KLUEPFEL
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Substrate Binding ◽  
Streptomyces Lividans ◽  
Cellulose Binding Domain ◽  
Binding Domains ◽  
New Family ◽  
Cellulose Binding ◽  
Sequence Similarities

The substrate-binding domains of six glycanases from Streptomyces lividans were investigated to determine their specificity towards cellulose and xylan. Based upon amino acid sequence similarities, four of the six domains could be assigned to existing cellulose-binding domain families. However, the binding domains of xylanase A and arabinofuranosidase B could not be classified in any of the known families and should therefore be classified as members of a new family. Evidence is also presented that this new family is one of true xylan-binding domains.

scholarly journals Human transcriptional activation domains require hydrophobic and acidic residues

2020 ◽  
Author(s):  
Max V. Staller ◽  
Eddie Ramirez ◽  
Alex S. Holehouse ◽  
Rohit V. Pappu ◽  
Barak A. Cohen
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Amino Acid Sequence ◽  
High Throughput ◽  
Design Principles ◽  
Structural Constraints ◽  
Activation Domains ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Acidic Residues

AbstractTranscription factors activate gene expression with separable DNA binding domains and activation domains (Latchman, 2008). High-throughput studies have uncovered rules for how DNA binding domains recognize their cognate DNA motifs, but the design principles of activation domains remain opaque. For over thirty years it has been a mystery why activation domains are acidic and unstructured (Sigler, 1988). Activation domains require hydrophobic motifs to bind coactivators and join transcriptional condensates, but low evolutionary conservation and intrinsic disorder have made it difficult to identify the design principles that govern the sequence to function relationship (Boija et al., 2018; Chong et al., 2018; Cress and Triezenberg, 1991; Dyson and Wright, 2016). Consequently, activation domains cannot be predicted from amino acid sequence (Finn et al., 2016). Here, we resolve the functional roles of acidity and disorder in activation domains and use these insights to build a new predictor. We designed sequence variants in seven acidic activation domains and measured their activities in parallel with a high-throughput assay in human cell culture. Our results support a flexible model in which acidic residues solubilize hydrophobic motifs so that they can interact with coactivators. This model accurately predicts activation domains in the human proteome. We identify three general rules for activation domain function: hydrophobic motifs must be balanced by acidic residues; acidic residues make large contributions to activity when they are adjacent to motifs; and within motifs, the presence of aromatic or leucine residues reflects the structural constraints of coactivator interactions. We anticipate these design principles will aid efforts to predict activations from amino acid sequence and to engineer new domains.

The Saccharomyces cerevisiae ACP2 gene encodes an essential HMG1-like protein

1988 ◽  
Vol 8 (3) ◽  
pp. 1282-1289
Author(s):  
W Haggren ◽  
D Kolodrubetz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
High Mobility ◽  
Hmg Proteins ◽  
Gene Encoding ◽  
Yeast Saccharomyces Cerevisiae ◽  
Dna Library ◽  
Associated Proteins ◽  
Genomic Dna Library

The high-mobility-group (HMG) proteins, a group of nonhistone chromatin-associated proteins, have been extensively characterized in higher eucaryotic cells. To test the biological function of an HMG protein, we have cloned and mutagenized a gene encoding an HMG-like protein from the yeast Saccharomyces cerevisiae. A yeast genomic DNA library was screened with an oligonucleotide designed to hybridize to any yeast gene containing an amino acid sequence conserved in several higher eucaryotic HMG proteins. DNA sequencing and Northern (RNA) blot analysis revealed that one gene, called ACP2 (acidic protein 2), synthesizes a poly(A)+ RNA in S. cerevisiae which encodes a 27,000-molecular-weight protein whose amino acid sequence is homologous to those of calf HMG1 and HMG2 and trout HMGT proteins. Standard procedures were used to construct a diploid yeast strain in which one copy of the ACP2 gene was mutated by replacement with the URA3 gene. When this diploid was sporulated and dissected, only half of the spores were viable. About half of the nonviable spores proceeded through two or three cell divisions and then stopped dividing; the rest did not germinate at all. None of the viable spores contained the mutant ACP2 gene, thus proving that the protein encoded by ACP2 is required for cell viability. The results presented here demonstrate that an HMG-like protein has an essential physiological function.

scholarly journals Amino acid sequence of the alpha subunit of human leukocyte adhesion receptor Mo1 (complement receptor type 3).

1988 ◽  
Vol 106 (6) ◽  
pp. 2153-2158 ◽  
Author(s):  
M A Arnaout ◽  
S K Gupta ◽  
M W Pierce ◽  
D G Tenen
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Metal Binding ◽  
Human Leukocyte ◽  
Receptor Type ◽  
Alpha Subunit ◽  
Complement Receptor ◽  
Complement Receptor Type ◽  
Binding Domains ◽  
Type 3

Mo1 (complement receptor type 3, CR3; CD11b/CD18) is an adhesion-promoting human leukocyte surface membrane heterodimer (alpha subunit 155 kD [CD11b] noncovalently linked to a beta subunit of 95 kD [CD18]). The complete amino acid sequence deduced from cDNA of the human alpha subunit is reported. The protein consists of 1,136 amino acids with a long amino-terminal extracytoplasmic domain, a 26-amino acid hydrophobic transmembrane segment, and a 19-carboxyl-terminal cytoplasmic domain. The extracytoplasmic region has three putative Ca2+-binding domains with good homology and one with weak homology to the "lock washer" Ca2+-binding consensus sequence. These metal-binding domains explain the divalent cation-dependent functions mediated by Mo1. The alpha subunit is highly homologous to the alpha subunit of leukocyte p150,95 and to a lesser extent, to the alpha subunit of other "integrin" receptors such as fibronectin, vitronectin, and platelet IIb/IIIa receptors in humans and position-specific antigen-2 (PS2) in Drosophila. Mo1 alpha, like p150, contains a unique 187-amino acid stretch NH2-terminal to the metal-binding domains. This region could be involved in some of the specific functions mediated by these leukocyte glycoproteins.

scholarly journals Molecular and genetic analyses of Drosophila Prat, which encodes the first enzyme of de novo purine biosynthesis.

Genetics ◽  
1994 ◽  
Vol 136 (2) ◽  
pp. 547-557 ◽  
Author(s):  
D V Clark
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
De Novo ◽  
Missense Mutations ◽  
Sequence Alignments ◽  
Nucleotide Biosynthesis ◽  
Amino Terminal ◽  
Binding Domains ◽  
De Novo Purine Biosynthesis ◽  
The Right

Abstract The Drosophila Prat gene encodes phosphoribosylamidotransferase (PRAT), the enzyme that performs the first committed step of the de novo purine nucleotide biosynthesis pathway. Using information from amino acid sequence alignments of PRAT from other organisms, a polymerase chain reaction-based approach was employed to clone Prat. Amino acid sequence alignment of Drosophila PRAT with PRAT from bacteria, yeast, and vertebrates indicates that it is most identical (at least 60%) to the vertebrate PRATs. It shares putative amino-terminal propeptide and iron-binding domains seen only in Bacillus subtilis and vertebrate PRATs. Prat was localized to the right arm of chromosome 3 at polytene band 84E1-2. Owing to the fact that this region had been well characterized previously, Prat was localized to a 30-kilobase region between two deficiency breakpoints. By making the prediction that Prat would have a similar "purine syndrome" phenotype as mutations in the genes ade2 and ade3, which encode enzymes downstream in the pathway, five alleles of Prat were isolated. Three of the alleles were identified as missense mutations. A comparison of PRAT enzyme activity with phenotype in three of the mutants indicates that a reduction to 40% of the wild-type allele's activity is sufficient to cause the purine syndrome, suggesting that PRAT activity is limiting in Drosophila.

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