Alignment and Searching for Common Protein Folds Using a Data Bank of Structural Templates

Johnson, Mark S.; Overington, John P.; Blundell, Tom L.

doi:10.1006/jmbi.1993.1323

Cited by 164 publications

(95 citation statements)

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“…The sequence alignment of avidin and AVR4/5 was done using MALIGN (34) in BODIL using a structure-based sequence comparison matrix (35) with gap-penalty 40.…”

Section: Mutagenesis Of Avr4/5 and The Purification Of Recombinantmentioning

confidence: 99%

Chicken Avidin-related Protein 4/5 Shows Superior Thermal Stability when Compared with Avidin while Retaining High Affinity to Biotin

Hytönen

Nyholm

Pentikäinen

et al. 2004

Journal of Biological Chemistry

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The protein chicken avidin is a commonly used tool in various applications. The avidin gene belongs to a gene family that also includes seven other members known as the avidin-related genes (AVR). We report here on the extremely high thermal stability and functional characteristics of avidin-related protein AVR4/5, a member of the avidin protein family. The thermal stability characteristics of AVR4/5 were examined using a differential scanning calorimeter, microparticle analysis, and a microplate assay. Its biotin-binding properties were studied using an isothermal calorimeter and IAsys optical biosensor. According to these analyses, in the absence of biotin AVR4/5 is clearly more stable (T m ‫؍‬ 107.4 ؎ 0.3°C) than avidin (T m ‫؍‬ 83.5 ؎ 0.1°C) or bacterial streptavidin (T m ‫؍‬ 75.5°C). AVR4/5 also exhibits a high affinity for biotin (K d Ϸ 3.6 ؋ 10 ؊14 M) comparable to that of avidin and streptavidin (K d Ϸ 10 ؊15 M). Molecular modeling and site-directed mutagenesis were used to study the molecular details behind the observed high thermostability. The results indicate that AVR4/5 and its mutants have high potential as new improved tools for applications where exceptionally high stability and tight biotin binding are needed.

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“…The sequence alignment of avidin and AVR4/5 was done using MALIGN (34) in BODIL using a structure-based sequence comparison matrix (35) with gap-penalty 40.…”

Section: Mutagenesis Of Avr4/5 and The Purification Of Recombinantmentioning

confidence: 99%

Chicken Avidin-related Protein 4/5 Shows Superior Thermal Stability when Compared with Avidin while Retaining High Affinity to Biotin

Hytönen

Nyholm

Pentikäinen

et al. 2004

Journal of Biological Chemistry

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“…In order to check for proteins of known three-dimensional structure that might be useful for modelling the 107 residue insert in HvAP, we used the computer programs QSLAVE and PSLAVE [32], which compare templates (either derived from structure or sequence) against a single sequence or a set of aligned sequences using the computer program MALIGN [21]. Structural templates have been constructed for the database of aligned three-dimensional structures of related proteins as well as individual structures [33].…”

Section: Structure Prediction Of the 'Large Insert' Between Gi#39 Andmentioning

confidence: 99%

Comparative modelling of barley‐grain aspartic proteinase: A structural rationale for observed hydrolytic specificity

et al. 1994

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A model of the barley-grain aspartic proteinase (HvAP; Hordeum vulgare aspartic proteinase) has been constructed using the rule-based comparative modelling approach encoded in the COMPOSER suite of computer programs. The model was based on the high resolution crystal structures of six highly homologous aspartic proteinases. Results suggest that the overall three-dimensional structure of HvAP (excluding the plant-specific insert; 104 residues in HvAP) is closer to human cathepsin D than other aspartic proteinases of known three-dimensional structure.

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“…A structural template was constructed for the erythrocruorin as described in Johnson et al (1993) where each position along the fold is described by environment-dependent amino acid substitution scores according to the local structural environment of the residue: the residue solvent accessibility and secondary structure. The template constructed from the single structure was searched against a databank of sequences containing 21,792 sequences >55 residues in length.…”

Section: Globin Searchesmentioning

confidence: 99%

“…In approaches introduced by Eisenberg and coworkers (Bowie et al, 1991;Liithy et al, 1991) and our own group Overington et al, 1990Overington et al, , 1992Johnson et al, 1993Johnson et al, , 1994a), 3D information is converted to a 1-dimensional (ID) description of the protein fold. A comparison then results from the matching of an amino acid sequence with these 1D representaReprint requests to: Mark S. Johnson at his present address: Centre for Biotechnology, P.O.…”

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confidence: 99%

Residue–Residue contact substitution probabilities derived from aligned three‐dimensional structures and the identification of common folds

Rodionov

Johnson

1994

Protein Science

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We report the derivation of scores that are based on the analysis of residue-residue contact matrices from 443 3-dimensional structures aligned structurally as 96 families, which can be used to evaluate sequence-structure matches. Residue-residue contacts and the more than 3 X lo6 amino acid substitutions that take place between pairs of these contacts at aligned positions within each family of structures have been tabulated and segregated according to the solvent accessibility of the residues involved. Contact maps within a family of structures are shown to be highly conserved (-75%) even when the sequence identity is approaching 10%. In a comparison involving a globin structure and the search of a sequence databank (>21,000 sequences), the contact probability scores are shown to provide a very powerful secondary screen for the top scoring sequence-structure matches, where between 69% and 84% of the unrelated matches are eliminated. The search of an aligned set of 2 globins against a sequence databank and the subsequent residue contact-based evaluation of matches locates all 618 globin sequences before the first non-globin match. From a single bacterial serine proteinase structure, the structural template approach coupled with residue-residue contact substitution data lead to the detection of the mammalian serine proteinase family among the top matches in the search of a sequence databank.

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Alignment and Searching for Common Protein Folds Using a Data Bank of Structural Templates

Cited by 164 publications

References 0 publications

Chicken Avidin-related Protein 4/5 Shows Superior Thermal Stability when Compared with Avidin while Retaining High Affinity to Biotin

Chicken Avidin-related Protein 4/5 Shows Superior Thermal Stability when Compared with Avidin while Retaining High Affinity to Biotin

Comparative modelling of barley‐grain aspartic proteinase: A structural rationale for observed hydrolytic specificity

Residue–Residue contact substitution probabilities derived from aligned three‐dimensional structures and the identification of common folds

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