scholarly journals InterPro: An integrated documentation resource for protein families, domains and functional sites

2002 ◽  
Vol 3 (3) ◽  
pp. 225-235 ◽  
Author(s):  
Keyword(s):  
Protein Families ◽  
Functional Sites

scholarly journals Functional Sites in Protein Families Uncovered via an Objective and Automated Graph Theoretic Approach

2003 ◽  
Vol 326 (3) ◽  
pp. 955-978 ◽  
Author(s):  
Pramod P. Wangikar ◽  
Ashish V. Tendulkar ◽  
S. Ramya ◽  
Deepali N. Mali ◽  
Sunita Sarawagi
Keyword(s):  
Theoretic Approach ◽  
Protein Families ◽  
Functional Sites ◽  
Graph Theoretic ◽  
Graph Theoretic Approach

scholarly journals InterPro--an integrated documentation resource for protein families, domains and functional sites

2000 ◽  
Vol 16 (12) ◽  
pp. 1145-1150 ◽  
Author(s):  
R. Apweiler ◽  
T. K. Attwood ◽  
A. Bairoch ◽  
A. Bateman ◽  
E. Birney ◽  
...  
Keyword(s):  
Protein Families ◽  
Functional Sites

scholarly journals InterPro (The Integrated Resource of Protein Domains and Functional Sites)

Yeast ◽  
2000 ◽  
Vol 1 (4) ◽  
pp. 327-334
Author(s):  
Christopher Southan
Keyword(s):  
Comparative Genomics ◽  
Protein Domains ◽  
Protein Family ◽  
European Bioinformatics Institute ◽  
Protein Families ◽  
Functional Sites ◽  
The Family ◽  
Graphic Displays

The family and motif databases, PROSITE, PRINTS, Pfam and ProDom, have been integrated into a powerful resource for protein secondary annotation. As of June 2000, InterPro had processed 384 572 proteins in SWISS-PROT and TrEMBL. Because the contributing databases have different clustering principles and scoring sensitivities, the combined assignments compliment each other for grouping protein families and delineating domains. The graphic displays of all matches above the scoring thresholds enables judgements to be made on the concordances or differences between the assignments. The website links can be used to analyse novel sequences and for queries across the proteomes of 32 organisms, including the partial human set, by domain and/or protein family. An analysis of selected HtrA/DegQ proteases demonstrates the utility of this website for detailed comparative genomics. Further information on the project can be found at the European Bioinformatics Institute at http://www.ebi.ac.uk/interpro/.

scholarly journals Origins of coevolution between residues distant in protein 3D structures

2017 ◽  
Vol 114 (34) ◽  
pp. 9122-9127 ◽  
Author(s):  
Ivan Anishchenko ◽  
Sergey Ovchinnikov ◽  
Hetunandan Kamisetty ◽  
David Baker
Keyword(s):  
Structure Prediction ◽  
Structural Variation ◽  
Protein Structures ◽  
Direct Coupling ◽  
Protein Families ◽  
Oligomeric State ◽  
3D Structures ◽  
Functional Sites ◽  
Repeat Proteins ◽  
The Family

Residue pairs that directly coevolve in protein families are generally close in protein 3D structures. Here we study the exceptions to this general trend—directly coevolving residue pairs that are distant in protein structures—to determine the origins of evolutionary pressure on spatially distant residues and to understand the sources of error in contact-based structure prediction. Over a set of 4,000 protein families, we find that 25% of directly coevolving residue pairs are separated by more than 5 Å in protein structures and 3% by more than 15 Å. The majority (91%) of directly coevolving residue pairs in the 5–15 Å range are found to be in contact in at least one homologous structure—these exceptions arise from structural variation in the family in the region containing the residues. Thirty-five percent of the exceptions greater than 15 Å are at homo-oligomeric interfaces, 19% arise from family structural variation, and 27% are in repeat proteins likely reflecting alignment errors. Of the remaining long-range exceptions (<1% of the total number of coupled pairs), many can be attributed to close interactions in an oligomeric state. Overall, the results suggest that directly coevolving residue pairs not in repeat proteins are spatially proximal in at least one biologically relevant protein conformation within the family; we find little evidence for direct coupling between residues at spatially separated allosteric and functional sites or for increased direct coupling between residue pairs on putative allosteric pathways connecting them.

mRNA localization by Electron microscopic in situ hybridization

1991 ◽  
Vol 49 ◽  
pp. 430-431
Author(s):  
J. A. Pollock ◽  
M. Martone ◽  
T. Deerinck ◽  
M. H. Ellisman
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Nucleic Acids ◽  
Recombinant Dna ◽  
Light And Electron Microscopy ◽  
Electron Microscopic ◽  
High Voltage Electron Microscopy ◽  
Functional Sites ◽  
Voltage Electron

Localization of specific proteins in cells by both light and electron microscopy has been facilitate by the availability of antibodies that recognize unique features of these proteins. High resolution localization studies conducted over the last 25 years have allowed biologists to study the synthesis, translocation and ultimate functional sites for many important classes of proteins. Recently, recombinant DNA techniques in molecular biology have allowed the production of specific probes for localization of nucleic acids by “in situ” hybridization. The availability of these probes potentially opens a new set of questions to experimental investigation regarding the subcellular distribution of specific DNA's and RNA's. Nucleic acids have a much lower “copy number” per cell than a typical protein, ranging from one copy to perhaps several thousand. Therefore, sensitive, high resolution techniques are required. There are several reasons why Intermediate Voltage Electron Microscopy (IVEM) and High Voltage Electron Microscopy (HVEM) are most useful for localization of nucleic acids in situ.

Importance of Protease Inhibition in Studies on Purified Factor VIII (Antihaemophilic Factor)

1976 ◽  
Vol 35 (01) ◽  
pp. 186-190 ◽  
Author(s):  
Eugen A. Beck ◽  
Peter Bachmann ◽  
Peter Barbier ◽  
Miha Furlan
Keyword(s):  
Ionic Strength ◽  
Factor Viii ◽  
Gel Filtration ◽  
High Ionic Strength ◽  
Procoagulant Activity ◽  
Carrier Protein ◽  
Protease Inhibition ◽  
Functional Sites ◽  
Molecular Weight Peak ◽  
Von Willebrand

SummaryAccording to some authors factor VIII procoagulant activity may be dissociable from carrier protein (MW~ 2 × 106) by agarose gel filtration, e.g. at high ionic strength. We were able to reproduce this phenomenon. However, addition of protease inhibitor (Trasylol) prevented the appearance of low molecular weight peak of factor VIII procoagulant activity both at high ionic strength and elevated temperature (37°C). We conclude from our results that procoagulant activity and carrier protein (von Willebrand factor, factor VIII antigen) are closely associated functional sites of native factor VIII macro molecule. Consequently, proteolytic degradation should be avoided in functional and structural studies on factor VIII and especially in preparing factor VIII concentrate for therapeutic use.

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