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Comparison of three-dimensional structures of homologous proteins
“Of particular interesV in the opinion of structural biologists. Papers “of particular
interest”
selected,
from the previous
year’s
literature, by the authors of reviews in the section on Sequences Topology
in the )une 1992 issue of Current
in Structural
and Biology.
Comparison of three-dimensional structures of homologous proteins selected by John P. Overington ZHU Z-Y, $hu A, BLIJNDEU TL- A Variable Gap Penalty Function and Feature Weights for Protein 3-D Structure Comparisons. Protein Eng 1992, 5:43-52. A development of the COMPARER program to include two u,sefi~lfeatures: the addition of a secondary structure and accessibility-profile-dependent gap penalty function for the optimized placement of gaps; and, rational assignment of the weights used for differing structural features in the comparison. VYAS NK, VVAS MN, QUI~CHO FA: Comparison of the Periplasmic Receptors for L-arabinose, D-@ucose/~gaIactose, and u-ribose: structural and functional similarity, J Siol Cbem 1991, 26652265237. in example of the use of the alignment of two distantly related proteins as a template for the alignment of the sequence for a further distantly related example of the Same fold. The paper also makes the salient point for homology modelling studies that the mode of substrate binding is not always conserved. 1Uimm’ KM, MCKAY DB, bE%CH W, Hews KC: Similarity of the Three-dimensional Structures of Actin and the ATPase Fragment of a 70kDa Heat Shock Cognate Protein. Proc Nut1 Acad Sci &J S A
J, B~RCKEKTN, COIIRI~ M, DLI PASQUIE:R L: The Ontogeny of Diversification at the ImmunogIobuiin Heavy Chain Locus in Xenoptls, IE3H30 J 191, l&2461-2470. Comparison of molecular basis for VI, diversification in tadpole and adult Xenqus,
1991, 88:5041-5045.
Serpina mobile conformations proteinase inhibitors selected Carrel1 and Dyfed L.1, Evans
comparison of the three-dimensional structures of actin and the heat-shock cognate protein ATPase fragment. The degree of structural similarity is really quite surprising, given the minimal sequence identity of the two A
sequenca.
Primary structure of immunoglobulins through evolution selected by Ellen fisu and Lisa A. Steiner HOHMAN VS, SCIILUL‘ER SF, MARCHALO~VIS JJ: Complete Sequence of a cDNA Clone Specifying Sandbar Shark Immunoglobulin Light Chain: Gene Organization and Implications for the Evolution of Light Chains. Pm Nd Acud Sci I/ $ A 1992, 89:2762GO. Seyjuence comparisons suggest that the shark light chain is a member of the A family. %i%‘AGER
j, BijRCKERT’
N,
SCHWAGER
M,
WILwN
M:
EVO-
lution of Immunoglobulin Light Chain Genes: Analysis of Xertopus IgL Isotypes and their Contribution to Antibody Diversity. EM13OJ 1991, 10:505-511. Dtxription of Xenoprti laev& light chains with V and C regions very dil-Ferent in sequence from those previously identified in mammals, birds, amphibians or sharks. 376
Opinion
SCI~AGER
Predicting de nova the folded structure proteins selected by Steven A. Benner
of
JU, LUTIN R, EISEM)ERG D: A Method to tdentily Protein Sequences that Fold into a Known Threedimensional Structure. Science 1991, 253: 164-170. A sophisticated implementation of a knowledge-based approach to modeling the folded structure of proteins. BOWIE
FINKELSTEIN AV, REVA BA: A Search for the Most Stable Folds of Protein Chains. N&we 1!3!31, 35 1:497-4!% An effort to construct an analysis of types of sequences that can form stable folds, KNIGHTON XUONG
DR, ZHENG JH, M-I,
TAYI.~R
SS,
TEN EYCK LF, ASH~;ORIJ VA, SOWADSKI JM: Crystal Struc-
ture of the Catalytic Subunit of Cyclic Adenosine Monophosphate-dependent Protein tinase. Science 1991, 253407-414.
The crystal structure
of the cataIytic domain of protein
kinascs.
in a family of by Robin W.
MOITONEN J, S’~RANIIA, SYMEMY J, S~E’T RM, DANLEY DE, GEOGHEGAN KF, GERARD RD, Gwmu-r*H EJ: Structural Basis of Latency in Plasminogen Activator Inhibitor- 1. Nature 1992, 355:2X--273. The solution of the structure of latent PAI-1 to 2.6W (R factor 19.8%) shows a full reincorporation of the reactivecentre loop into the A sheet with a linked release of strand 1 from the C sheet. SKIUW K, WIKOFI: WR, PATSON PA, TAUSK F, SCHAPIRA M, KUUN AI), BOCK SC: Substrate Properties of CIBar Inhibitor Ma (Alanine 434 3 Glutamic Acid). Genetic and Structural Evidence Suggesting that the Plz-Region Contains Critical Determinants of Serine Protease Inhibitor/Substrate Status. .I Siol Cbem 1991,
26692 16-922 1.
Evidence from dysfUnctiona P 12 mutant and other studies of C, -inhibitor supports partial reincorporation of strand A4 as a requirement for inhibitoy activity. Modelling suggests linkage of movement of loop to strand 3 of the C sheet. @ 1992 Current
Biology
interest”
selected,
from the previous
year’s
literature, by the authors of reviews in the section on Sequences Topology
in the )une 1992 issue of Current
in Structural
and Biology.
Comparison of three-dimensional structures of homologous proteins selected by John P. Overington ZHU Z-Y, $hu A, BLIJNDEU TL- A Variable Gap Penalty Function and Feature Weights for Protein 3-D Structure Comparisons. Protein Eng 1992, 5:43-52. A development of the COMPARER program to include two u,sefi~lfeatures: the addition of a secondary structure and accessibility-profile-dependent gap penalty function for the optimized placement of gaps; and, rational assignment of the weights used for differing structural features in the comparison. VYAS NK, VVAS MN, QUI~CHO FA: Comparison of the Periplasmic Receptors for L-arabinose, D-@ucose/~gaIactose, and u-ribose: structural and functional similarity, J Siol Cbem 1991, 26652265237. in example of the use of the alignment of two distantly related proteins as a template for the alignment of the sequence for a further distantly related example of the Same fold. The paper also makes the salient point for homology modelling studies that the mode of substrate binding is not always conserved. 1Uimm’ KM, MCKAY DB, bE%CH W, Hews KC: Similarity of the Three-dimensional Structures of Actin and the ATPase Fragment of a 70kDa Heat Shock Cognate Protein. Proc Nut1 Acad Sci &J S A
J, B~RCKEKTN, COIIRI~ M, DLI PASQUIE:R L: The Ontogeny of Diversification at the ImmunogIobuiin Heavy Chain Locus in Xenoptls, IE3H30 J 191, l&2461-2470. Comparison of molecular basis for VI, diversification in tadpole and adult Xenqus,
1991, 88:5041-5045.
Serpina mobile conformations proteinase inhibitors selected Carrel1 and Dyfed L.1, Evans
comparison of the three-dimensional structures of actin and the heat-shock cognate protein ATPase fragment. The degree of structural similarity is really quite surprising, given the minimal sequence identity of the two A
sequenca.
Primary structure of immunoglobulins through evolution selected by Ellen fisu and Lisa A. Steiner HOHMAN VS, SCIILUL‘ER SF, MARCHALO~VIS JJ: Complete Sequence of a cDNA Clone Specifying Sandbar Shark Immunoglobulin Light Chain: Gene Organization and Implications for the Evolution of Light Chains. Pm Nd Acud Sci I/ $ A 1992, 89:2762GO. Seyjuence comparisons suggest that the shark light chain is a member of the A family. %i%‘AGER
j, BijRCKERT’
N,
SCHWAGER
M,
WILwN
M:
EVO-
lution of Immunoglobulin Light Chain Genes: Analysis of Xertopus IgL Isotypes and their Contribution to Antibody Diversity. EM13OJ 1991, 10:505-511. Dtxription of Xenoprti laev& light chains with V and C regions very dil-Ferent in sequence from those previously identified in mammals, birds, amphibians or sharks. 376
Opinion
SCI~AGER
Predicting de nova the folded structure proteins selected by Steven A. Benner
of
JU, LUTIN R, EISEM)ERG D: A Method to tdentily Protein Sequences that Fold into a Known Threedimensional Structure. Science 1991, 253: 164-170. A sophisticated implementation of a knowledge-based approach to modeling the folded structure of proteins. BOWIE
FINKELSTEIN AV, REVA BA: A Search for the Most Stable Folds of Protein Chains. N&we 1!3!31, 35 1:497-4!% An effort to construct an analysis of types of sequences that can form stable folds, KNIGHTON XUONG
DR, ZHENG JH, M-I,
TAYI.~R
SS,
TEN EYCK LF, ASH~;ORIJ VA, SOWADSKI JM: Crystal Struc-
ture of the Catalytic Subunit of Cyclic Adenosine Monophosphate-dependent Protein tinase. Science 1991, 253407-414.
The crystal structure
of the cataIytic domain of protein
kinascs.
in a family of by Robin W.
MOITONEN J, S’~RANIIA, SYMEMY J, S~E’T RM, DANLEY DE, GEOGHEGAN KF, GERARD RD, Gwmu-r*H EJ: Structural Basis of Latency in Plasminogen Activator Inhibitor- 1. Nature 1992, 355:2X--273. The solution of the structure of latent PAI-1 to 2.6W (R factor 19.8%) shows a full reincorporation of the reactivecentre loop into the A sheet with a linked release of strand 1 from the C sheet. SKIUW K, WIKOFI: WR, PATSON PA, TAUSK F, SCHAPIRA M, KUUN AI), BOCK SC: Substrate Properties of CIBar Inhibitor Ma (Alanine 434 3 Glutamic Acid). Genetic and Structural Evidence Suggesting that the Plz-Region Contains Critical Determinants of Serine Protease Inhibitor/Substrate Status. .I Siol Cbem 1991,
26692 16-922 1.
Evidence from dysfUnctiona P 12 mutant and other studies of C, -inhibitor supports partial reincorporation of strand A4 as a requirement for inhibitoy activity. Modelling suggests linkage of movement of loop to strand 3 of the C sheet. @ 1992 Current
Biology