Comparison of Naturally Occurring Vitamin K-Dependent Proteins:  Correlation of Amino Acid Sequences and Membrane Binding Properties Suggests a Membrane Contact Site†

Calcium and phospholipid binding proteins have been identified and localized by immunocytochemistry in a wide range of cells and tissues. Two of these proteins (calpactins) also bind F-actin and are substrates for tyrosine kinases. The similar membrane-binding properties of these molecules arise from conserved amino acid sequences and a model is proposed for the tertiary structure of a common calcium and phospholipid binding domain.

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Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798321003417 ◽

2021 ◽

Vol 77 (5) ◽

pp. 690-702

Author(s):

Pandian Ramesh ◽

Selvarajan Sigamani Sundaresan ◽

Nagaraj Shobana ◽

Thangaraj Vinuchakkaravarthy ◽

Kandasamy Sivakumar ◽

...

Keyword(s):

Amino Acid ◽

Structural Features ◽

Crystal Structure Analysis ◽

Oxygen Molecule ◽

Amino Acid Sequences ◽

Physical Parameters ◽

Oxygen Binding ◽

Binding Properties ◽

Form Analysis ◽

Inverse Transition

Crystal structures of hemoglobin (Hb) from two flightless birds, ostrich (Struthio camelus) and turkey (Meleagris gallopova), were determined. The ostrich Hb structure was solved to a resolution of 2.22 Å, whereas two forms of turkey Hb were solved to resolutions of 1.66 Å (turkey monoclinic structure; TMS) and 1.39 Å (turkey orthorhombic structure; TOS). Comparison of the amino-acid sequences of ostrich and turkey Hb with those from other avian species revealed no difference in the number of charged residues, but variations were observed in the numbers of hydrophobic and polar residues. Amino-acid-composition-based computation of various physical parameters, in particular their lower inverse transition temperatures and higher average hydrophobicities, indicated that the structures of ostrich and turkey Hb are likely to be highly ordered when compared with other avian Hbs. From the crystal structure analysis, the liganded state of ostrich Hb was confirmed by the presence of an oxygen molecule between the Fe atom and the proximal histidine residue in all four heme regions. In turkey Hb (both TMS and TOS), a water molecule was bound instead of an oxygen molecule in all four heme regions, thus confirming that they assumed the aqua-met form. Analysis of tertiary- and quaternary-structural features led to the conclusion that ostrich oxy Hb and turkey aqua-met Hb adopt the R-/RH-state conformation.

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A Contact Site between the Two Reaction Center Polypeptides of Photosystem II Is Involved in Photoinhibition

Zeitschrift für Naturforschung C ◽

10.1515/znc-1991-7-809 ◽

1991 ◽

Vol 46 (7-8) ◽

pp. 557-562 ◽

Cited By ~ 36

Author(s):

A. Trebst

Keyword(s):

Amino Acid ◽

Photosystem Ii ◽

Reaction Center ◽

Binding Sites ◽

Cleavage Site ◽

Amino Acid Sequences ◽

Contact Site ◽

Quinone Binding ◽

Herbicide Binding ◽

Sensitive Site

Abstract A new contact site between the two reaction center polypeptides D 1 and D 2 of photosystem II close to arg 238 and arg 234 respectively is proposed. The amino acid sequences involved are between the 4 th transmembrane and a connecting parallel helix. The sequence includes a tryp sin sensitive site in both polypeptides, the likely cleavage site in the rapid turnover of the D 1 polypeptide and part of the herbicide binding site. The contact site is oriented towards both quinone binding sites Q A and Q B. A folding of the backbone of the amino acid sequences involved is proposed.

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Thousands of protein linear motif classes may still be undiscovered

PLoS ONE ◽

10.1371/journal.pone.0248841 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0248841

Author(s):

Denys Bulavka ◽

Ariel A. Aptekmann ◽

Nicolás A. Méndez ◽

Teresa Krick ◽

Ignacio E. Sánchez

Keyword(s):

Amino Acid ◽

Protein Interactions ◽

Amino Acid Sequences ◽

Linear Motif ◽

Motif Length ◽

Naturally Occurring ◽

Motif Position ◽

Linear Motifs ◽

Short Protein ◽

Amino Acid Alphabet

Linear motifs are short protein subsequences that mediate protein interactions. Hundreds of motif classes including thousands of motif instances are known. Our theory estimates how many motif classes remain undiscovered. As commonly done, we describe motif classes as regular expressions specifying motif length and the allowed amino acids at each motif position. We measure motif specificity for a pair of motif classes by quantifying how many motif-discriminating positions prevent a protein subsequence from matching the two classes at once. We derive theorems for the maximal number of motif classes that can simultaneously maintain a certain number of motif-discriminating positions between all pairs of classes in the motif universe, for a given amino acid alphabet. We also calculate the fraction of all protein subsequences that would belong to a motif class if all potential motif classes came into existence. Naturally occurring pairs of motif classes present most often a single motif-discriminating position. This mild specificity maximizes the potential number of coexisting motif classes, the expansion of the motif universe due to amino acid modifications and the fraction of amino acid sequences that code for a motif instance. As a result, thousands of linear motif classes may remain undiscovered.

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Studies on Monotreme Proteins. IV Amino Acid Sequence of Haemoglobin-IA of the Echidna; A Comparison of Major Haemoglobins From Two Geographical Groups of Echidnas

Australian Journal of Biological Sciences ◽

10.1071/bi9740111 ◽

1974 ◽

Vol 27 (2) ◽

pp. 111 ◽

Cited By ~ 3

Author(s):

SJ Dodgson ◽

WK Fisher ◽

EOP Thompson

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Amino Acid Sequences ◽

Contact Site ◽

Acidic Group ◽

Phoretic Mobility ◽

Geographically Isolated

The amino acid sequences of the ex-and fJ-chains from a major haemoglobin (Hb-IA) of an echidna geographically isolated from those animals previously studied have been determined. The fJ-chain of Hb-IA was identical in amino acid sequence with the fJ-chain in Hb-IB. The ex-chain of Hb-IA varied in four positions from that in Hb-IB, and had one more acidic group, in line with the higher electro-phoretic mobility of Hb-IA at pH 8� 5. There were no differences in 'contact site' residues in the ex-chains of the two haemoglobins.

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Amino acid sequences and calcium-binding properties of two isoforms of barnacle troponin C

Biochemistry ◽

10.1021/bi00217a017 ◽

1991 ◽

Vol 30 (3) ◽

pp. 702-707 ◽

Cited By ~ 37

Author(s):

John H. Collins ◽

Janet L. Theibert ◽

Jean Marie Francois ◽

C. C. Ashley ◽

James D. Potter

Keyword(s):

Amino Acid ◽

Calcium Binding ◽

Troponin C ◽

Amino Acid Sequences ◽

Binding Properties

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Comparison of complete amino acid sequences and receptor-binding properties among 13 serotypes of hemagglutinins of influenza A viruses

Virology ◽

10.1016/0042-6822(91)90588-3 ◽

1991 ◽

Vol 182 (2) ◽

pp. 475-485 ◽

Cited By ~ 334

Author(s):

E. Nobusawa ◽

T. Aoyama ◽

H. Kato ◽

Y. Suzuki ◽

Y. Tateno ◽

...

Keyword(s):

Amino Acid ◽

Receptor Binding ◽

Influenza A ◽

Amino Acid Sequences ◽

Influenza A Viruses ◽

Binding Properties

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The Surface Glycoproteins of H5 Influenza Viruses Isolated from Humans, Chickens, and Wild Aquatic Birds Have Distinguishable Properties

Journal of Virology ◽

10.1128/jvi.73.2.1146-1155.1999 ◽

1999 ◽

Vol 73 (2) ◽

pp. 1146-1155 ◽

Cited By ~ 409

Author(s):

Mikhail Matrosovich ◽

Nannan Zhou ◽

Yoshihiro Kawaoka ◽

Robert Webster

Keyword(s):

Hong Kong ◽

Amino Acid ◽

Amino Acid Sequences ◽

Influenza Viruses ◽

Amino Acid Deletion ◽

Aquatic Birds ◽

Avian Influenza Viruses ◽

Binding Properties ◽

Characteristic Features ◽

First Time

ABSTRACT In 1997, 18 confirmed cases of human influenza arising from multiple independent transmissions of H5N1 viruses from infected chickens were reported from Hong Kong. To identify possible phenotypic changes in the hemagglutinin (HA) and neuraminidase (NA) of the H5 viruses during interspecies transfer, we compared the receptor-binding properties and NA activities of the human and chicken H5N1 isolates from Hong Kong and of H5N3 and H5N1 viruses from wild aquatic birds. All H5N1 viruses, including the human isolate bound to Sia2-3Gal-containing receptors but not to Sia2-6Gal-containing receptors. This finding formally demonstrates for the first time that receptor specificity of avian influenza viruses may not restrict initial avian-to-human transmission. The H5N1 chicken viruses differed from H5 viruses of wild aquatic birds by a 19-amino-acid deletion in the stalk of the NA and the presence of a carbohydrate at the globular head of the HA. We found that a deletion in the NA decreased its ability to release the virus from cells, whereas carbohydrate at the HA head decreased the affinity of the virus for cell receptors. Comparison of amino acid sequences from GenBank of the HAs and NAs from different avian species revealed that additional glycosylation of the HA and a shortened NA stalk are characteristic features of the H5 and H7 chicken viruses. This finding indicates that changes in both HA and NA may be required for the adaptation of influenza viruses from wild aquatic birds to domestic chickens and raises the possibility that chickens may be a possible intermediate host in zoonotic transmission.

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Serum Resistance in Haemophilus ducreyiRequires Outer Membrane Protein DsrA

Infection and Immunity ◽

10.1128/iai.68.3.1608-1619.2000 ◽

2000 ◽

Vol 68 (3) ◽

pp. 1608-1619 ◽

Cited By ~ 73

Author(s):

Christopher Elkins ◽

K. John Morrow ◽

Bonnie Olsen

Keyword(s):

Amino Acid ◽

Membrane Protein ◽

Outer Membrane ◽

Outer Membrane Protein ◽

Polyacrylamide Gel Electrophoresis ◽

Sodium Dodecyl ◽

Serum Antibody ◽

Amino Acid Sequences ◽

Serum Resistance ◽

Naturally Occurring

ABSTRACT Haemophilus ducreyi is resistant to killing by normal serum antibody and complement. We discovered an H. ducreyiouter membrane protein required for expression of serum resistance and termed it DsrA (for “ducreyi serum resistance A”). ThedsrA locus was cloned, sequenced, and mutagenized. An isogenic mutant (FX517) of parent strain 35000 was constructed and characterized, and it was found to no longer express dsrA. FX517 was at least 10-fold more serum susceptible than 35000. DsrA was expressed by all strains of H. ducreyi tested, except three naturally occurring, avirulent, serum-sensitive strains. FX517 and the three naturally occurring dsrA-nonexpressing strains were complemented in trans with a plasmid expressingdsrA. All four strains were converted to a serum-resistant phenotype, including two that contained truncated lipooligosaccharide (LOS). Therefore, serum resistance in H. ducreyi does not require expression of full-length LOS but does require expression ofdsrA. The dsrA locus from eight additionalH. ducreyi strains was sequenced, and the deduced amino acid sequences were more than 85% identical. The major difference between the DsrA proteins was due to the presence of one, two, or three copies of the heptameric amino acid repeat NTHNINK. These repeats account for the variability in apparent molecular mass of the monomeric form of DsrA (28 to 35 kDa) observed in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Since DsrA is present in virulent strains, is highly conserved, and is required for serum resistance, we speculate that it may be a virulence factor and a potential vaccine candidate.

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