scholarly journals ASTRO-FOLD: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence

2003 ◽  
Vol 85 (4) ◽  
pp. 2119-2146 ◽  
Author(s):  
J.L. Klepeis ◽  
C.A. Floudas
Keyword(s):  
Global Optimization ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Ab Initio ◽  
Three Dimensional ◽  
Optimization Framework ◽  
Ab Initio Prediction

scholarly journals The covalent and three-dimensional structural of concanavalin A. I. Amino acid sequence of cyanogen bromide fragments F1 and F2.

1975 ◽  
Vol 250 (4) ◽  
pp. 1490-1502 ◽  
Author(s):  
J L Wang ◽  
B A Cunningham ◽  
M J Waxdal ◽  
G M Edelman
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Concanavalin A ◽  
Cyanogen Bromide ◽  
Three Dimensional

scholarly journals Cloning, expression and map assignment of chicken prosaposin

1998 ◽  
Vol 330 (1) ◽  
pp. 321-327 ◽  
Author(s):  
Norihiro AZUMA ◽  
Hee-Chan SEO ◽  
Øystein LIE ◽  
Qiang FU ◽  
M. Robert GOULD ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Mammalian Species ◽  
Three Dimensional ◽  
Glycosylation Site ◽  
Amino Acid Sequences ◽  
Predicted Amino Acid Sequence ◽  
Chicken Brain ◽  
Saposin C ◽  
Saposin B

Prosaposin is the precursor of four small glycoproteins, saposins A-D, that activate lysosomal sphingolipid hydrolysis. A full-length cDNA encoding prosaposin from chicken brain was isolated by PCR. The deduced amino acid sequence predicted that, similarly to human and other mammalian species studied, chicken prosaposin contains 518 residues, including four domains that correspond to saposins A-D. There was 59% identity and 76% similarity of human and chicken prosaposin amino acid sequences. The basic three-dimensional structures of these saposins is predicted to be similar on the basis of the conservation of six cysteine residues and an N-glycosylation site. Identity of amino acid sequences was higher among saposins A, B and D than in saposin C. The predicted amino acid sequence of saposin B matched exactly that of purified chicken saposin B protein. The chicken prosaposin gene was mapped to a single locus, PSAP, in chicken linkage group E11C10 and is closely linked to the ACTA2 locus. This confirms the homology between chicken and human prosaposins and defines a new conserved segment with human chromosome 10q21-q24.

scholarly journals Amino acid sequence and three-dimensional structure of the Tn-specific isolectin B4 fromVicia villosa

FEBS Letters ◽  
1997 ◽  
Vol 412 (1) ◽  
pp. 190-196 ◽  
Author(s):  
Eduardo Osinaga ◽  
Diana Tello ◽  
Carlos Batthyany ◽  
Mario Bianchet ◽  
Gisele Tavares ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Isolectin B4

scholarly journals Expression, purification and crystallization of a protein resulting from the inversion of the amino-acid sequence of a helical bundle

2017 ◽  
Vol 73 (1) ◽  
pp. 51-53
Author(s):  
Aikaterini Kefala ◽  
Dina Kotsifaki ◽  
Mary Providaki ◽  
Maria Amprazi ◽  
Michael Kokkinidis
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Three Dimensional ◽  
Unfolded Proteins ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Helical Bundle ◽  
Sequence Inversion ◽  
The Impact

Earlier studies have found that the occurrence of inverse sequence identity in proteins is not indicative of three-dimensional similarity, but rather leads to different folds or unfolded proteins. Short helices, however, frequently keep their conformations when their sequences are inverted. To explore the impact of sequence inversion on long helices, revRM6, with the inverse amino-acid sequence relative to RM6, a highly stable variant of the ColE1 Rop protein, was engineered. RM6 is a highly regular four-α-helical bundle that serves as a model system for protein-folding studies. Here, the crystallization and preliminary crystallographic characterization of revRM6 are reported. The protein was overexpressed inEscherichia coli, purified to homogeneity and crystallized. The crystals belonged to space groupP41212, with unit-cell parametersa=b= 44.98,c= 159.74 Å, and diffracted to a resolution of 3.45 Å.

scholarly journals Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (Tāpirins) from Extremely Thermophilic Caldicellulosiruptor Species

2018 ◽  
Vol 85 (3) ◽  
Author(s):  
Laura L. Lee ◽  
William S. Hart ◽  
Vladimir V. Lunin ◽  
Markus Alahuhta ◽  
Yannick J. Bomble ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Microcrystalline Cellulose ◽  
Binding Proteins ◽  
Amino Acid Sequence Identity ◽  
Plant Biomass ◽  
Three Dimensional ◽  
Content Type ◽  
Sequence Identity ◽  
Cellulose Binding

ABSTRACT Genomes of extremely thermophilic Caldicellulosiruptor species encode novel cellulose binding proteins, called tāpirins, located proximate to the type IV pilus locus. The C-terminal domain of Caldicellulosiruptor kronotskyensis tāpirin 0844 (Calkro_0844) is structurally unique and has a cellulose binding affinity akin to that seen with family 3 carbohydrate binding modules (CBM3s). Here, full-length and C-terminal versions of tāpirins from Caldicellulosiruptor bescii (Athe_1870), Caldicellulosiruptor hydrothermalis (Calhy_0908), Caldicellulosiruptor kristjanssonii (Calkr_0826), and Caldicellulosiruptor naganoensis (NA10_0869) were produced recombinantly in Escherichia coli and compared to Calkro_0844. All five tāpirins bound to microcrystalline cellulose, switchgrass, poplar, and filter paper but not to xylan. Densitometry analysis of bound protein fractions visualized by SDS-PAGE revealed that Calhy_0908 and Calkr_0826 (from weakly cellulolytic species) associated with the cellulose substrates to a greater extent than Athe_1870, Calkro_0844, and NA10_0869 (from strongly cellulolytic species). Perhaps this relates to their specific needs to capture glucans released from lignocellulose by cellulases produced in Caldicellulosiruptor communities. Calkro_0844 and NA10_0869 share a higher degree of amino acid sequence identity (>80% identity) with each other than either does with Athe_1870 (∼50%). The levels of amino acid sequence identity of Calhy_0908 and Calkr_0826 to Calkro_0844 were only 16% and 36%, respectively, although the three-dimensional structures of their C-terminal binding regions were closely related. Unlike the parent strain, C. bescii mutants lacking the tāpirin genes did not bind to cellulose following short-term incubation, suggesting a role in cell association with plant biomass. Given the scarcity of carbohydrates in neutral terrestrial hot springs, tāpirins likely help scavenge carbohydrates from lignocellulose to support growth and survival of Caldicellulosiruptor species. IMPORTANCE The mechanisms by which microorganisms attach to and degrade lignocellulose are important to understand if effective approaches for conversion of plant biomass into fuels and chemicals are to be developed. Caldicellulosiruptor species grow on carbohydrates from lignocellulose at elevated temperatures and have biotechnological significance for that reason. Novel cellulose binding proteins, called tāpirins, are involved in the way that Caldicellulosiruptor species interact with microcrystalline cellulose, and additional information about the diversity of these proteins across the genus, including binding affinity and three-dimensional structural comparisons, is provided here.

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