scholarly journals Prediction and Fourier-transform infrared-spectroscopy estimation of the secondary structure of a recombinant β-glucosidase from Streptomyces sp. (ATCC 11238)

1995 ◽  
Vol 308 (3) ◽  
pp. 791-794 ◽  
Author(s):  
J A Perez-Pons ◽  
E Padros ◽  
E Querol
Keyword(s):  
Fourier Transform ◽  
Secondary Structure ◽  
Alpha Helix ◽  
Beta Sheet ◽  
Computer Algorithms ◽  
Computer Prediction ◽  
Ordered Structures ◽  
Streptomyces Sp ◽  
Helix 23 ◽  
Beta Glucosidase

The secondary structure of a recombinant beta-glucosidase (EC 3.2.1.21) from Streptomyces sp. (ATCC 11238) has been predicted by computer algorithms and also estimated by Fourier-transform IR spectroscopy. From curve fitting of the deconvoluted IR spectra, the most probable distribution of the secondary-structural classes appears to be about 34% alpha-helix, 30% beta-sheet, 25% reverse turns and 11% non-ordered structures. These data showed a good agreement with data from computer prediction (35% alpha-helix, 23% beta-sheet, 31% reverse turns and 11% non-ordered structures).

scholarly journals A comparison of the secondary structure of human brain mitochondrial and cytosolic ‘malic’ enzyme investigated by Fourier-transform infrared spectroscopy

1995 ◽  
Vol 309 (2) ◽  
pp. 607-611 ◽  
Author(s):  
Z Kochan ◽  
J Karbowska ◽  
G Bukato ◽  
M M Zydowo ◽  
E Bertoli ◽  
...  
Keyword(s):  
Fourier Transform ◽  
Secondary Structure ◽  
Human Brain ◽  
Ir Spectra ◽  
Conformational Changes ◽  
Malic Enzyme ◽  
Tertiary Structure ◽  
Alpha Helix ◽  
Random Structure ◽  
Mitochondrial Enzymes

The secondary structure of human brain cytosolic and mitochondrial ‘malic’ enzymes purified to homogeneity has been investigated by Fourier-transform IR spectroscopy. The absorbance IR spectra of these two isoenzymes were slightly different, but calculated secondary-structure compositions were essentially similar (38% alpha-helix, 38-39% beta-sheet, 14% beta-turn and 9-10% random structure). These proportions were not affected by succinate, a positive effector of mitochondrial ‘malic’ enzyme activity. IR spectra indicate that the tertiary structures of human brain cytosolic and mitochondrial ‘malic’ enzymes are slightly different, and addition of succinate does not cause conformational changes to the tertiary structure of the mitochondrial enzyme. Thermal-denaturation patterns of the cytosolic and mitochondrial enzymes, obtained from spectra recorded at different temperatures in the absence or presence of Mg2+, suggest that the tertiary structure of both isoenzymes is stabilized by bivalent cations and that the cytosolic enzyme possesses a more compact tertiary structure.

scholarly journals The secondary structure of protein G′, a robust molecule

1991 ◽  
Vol 274 (2) ◽  
pp. 503-507 ◽  
Author(s):  
C R Goward ◽  
L I Irons ◽  
J P Murphy ◽  
T Atkinson
Keyword(s):  
Biological Activity ◽  
Secondary Structure ◽  
Fluorescence Emission ◽  
Alpha Helix ◽  
Time Dependent ◽  
Protein G ◽  
Beta Sheet ◽  
Guanidinium Chloride ◽  
Streptococcal Protein G

The secondary structure of recombinant streptococcal Protein G' was predicted and compared with spectropolarimetric data. The predicted secondary structure consisted of 37 +/- 4% alpha-helix and 30 +/- 5% beta-sheet, whereas the values obtained from c.d. data were 29 +/- 2% alpha-helix and 41 +/- 3% beta-sheet. An alpha-helix-beta-sheet/turn-alpha-helix motif is conjectured to comprise the Fc-binding unit. The c.d. spectra in the near u.v. and far u.v. show that the Protein G' molecule is stable to heating at 100 degrees C and to extremes of pH (pH 1.5 to 11.0). The protein retained biological activity at these extremes. The molecule uncoils above pH 11.5 in a time-dependent fashion. Unfolding of the molecule in guanidinium chloride was monitored by c.d. and fluorescence emission; 3 M-guanidinium chloride was required to unfold the protein by 50%. The protein was completely unfolded in 5.5 M-guanidinium chloride and fully refolded with restoration of activity after removal of guanidinium chloride.

scholarly journals The predicted secondary structure of enolase

1986 ◽  
Vol 236 (1) ◽  
pp. 127-130 ◽  
Author(s):  
L Sawyer ◽  
L A Fothergill-Gilmore ◽  
G A Russell
Keyword(s):  
Skeletal Muscle ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Alpha Helix ◽  
Beta Sheet ◽  
Secondary Structure Content ◽  
Reverse Turn ◽  
Yeast Enolase ◽  
Chicken Skeletal Muscle

The results of several secondary-structure prediction programs were combined to produce an estimate of the regions of alpha-helix, beta-sheet and reverse turn for both chicken skeletal-muscle and yeast enolase sequences. The predicted secondary-structure content of the chicken enzyme is 27% alpha-helix and less than 10% beta-sheet, whereas in the yeast enolase a similar helix content but virtually no sheet are predicted. These results are in fair agreement with published experimental estimates of the amount of secondary structure in the yeast enzyme. The enzyme appears to be formed from three domains.

Biphasic effects of alcohols on the phase transition of poly(L-lysine) between .alpha.-helix and .beta.-sheet conformations

Biochemistry ◽  
1992 ◽  
Vol 31 (25) ◽  
pp. 5728-5733 ◽  
Author(s):  
Akira Shibata ◽  
Miharu Yamamoto ◽  
Takuya Yamashita ◽  
Jang Shing Chiou ◽  
Hiroshi Kamaya ◽  
...  
Keyword(s):  
Phase Transition ◽  
Alpha Helix ◽  
Beta Sheet

scholarly journals Characterization of porcine osteonectin extracted from foetal calvariae

1988 ◽  
Vol 253 (1) ◽  
pp. 139-151 ◽  
Author(s):  
C Domenicucci ◽  
H A Goldberg ◽  
T Hofmann ◽  
D Isenman ◽  
S Wasi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Type I Collagen ◽  
Culture Shock ◽  
Gel Filtration ◽  
Alpha Helix ◽  
Type I ◽  
Homologous Proteins ◽  
Compact Structure ◽  
Significant Difference

Osteonectin, extracted from foetal porcine calvariae with 0.5 M-EDTA, was purified to homogeneity by using gel filtration and polyanion anion-exchange fast protein liquid chromatography under dissociative conditions without the need of reducing agents. The purified protein migrated with an Mr of 40,300 on SDS/polyacrylamide gels and was similar to bovine osteonectin in both amino acid composition and in its ability to bind to hydroxyapatite in the presence of 4 M-guanidinium hydrochloride (GdmCl). However, unlike the bovine protein, porcine osteonectin did not bind selectively to hydroxyapatite when EDTA tissue extracts were used. In addition, purified porcine osteonectin did not show any apparent affinity for either native or denatured type I collagen, but did bind to serum albumin. Primary sequence analysis revealed an N-terminal alanine residue, with approximately one-half of the subsequent 35 residues identified as small hydrophobic amino acids and one-quarter as acidic amino acids. The only significant difference between the N-terminal sequences of the bovine and porcine proteins was the deletion of the tripeptide Val-Ala-Glu in porcine osteonectin. In contrast with bovine osteonectin, far-u.v.c.d. of porcine osteonectin revealed considerable secondary structure, of which 27% was alpha-helix and 39% was beta-sheet. Cleavage of the molecule with CNBr under non-reducing conditions generated five fragments, of which two major fragments (Mr 27,900 and 12,400) stained blue with Stains All, a reagent that stains sialic-acid-rich proteins/phosphate-containing proteins and/or Ca2+-binding proteins blue while staining other proteins pink. The 12,400-Mr fragment bound 45Ca2+ selectively, indicating a Ca2+-binding site in this part of the molecule. The 27,900-Mr fragment did not bind Ca2+, and since biosynthetic studies with 32PO4(3-) did not show phosphorylation of porcine osteonectin, this fragment is likely to be highly acidic. The incomplete cleavage of the molecule with CNBr and the ability of the molecule to regain its secondary structure after exposure to 7 M-urea are features consistent with the molecule having a compact structure that is stabilized by numerous disulphide bridges. The chemical and binding properties of porcine osteonectin are closely similar to the recently described ‘culture shock’, SPARC and BM-40 proteins, indicating that these are homologous proteins.

scholarly journals “In Silico” Characterization of 3-Phytase A and 3-Phytase B from Aspergillus niger

2017 ◽  
Vol 2017 ◽  
pp. 1-23 ◽  
Author(s):  
Doris C. Niño-Gómez ◽  
Claudia M. Rivera-Hoyos ◽  
Edwin D. Morales-Álvarez ◽  
Edgar A. Reyes-Montaño ◽  
Nury E. Vargas-Alejo ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Phytic Acid ◽  
Aqueous Media ◽  
Alpha Helix ◽  
Proton Donor ◽  
Van Der Waals Interactions ◽  
Beta Sheet ◽  
Instability Index ◽  
Bioinformatic Tools ◽  
Helix 12

Phytases are used for feeding monogastric animals, because they hydrolyze phytic acid generating inorganic phosphate. Aspergillus niger 3-phytase A (PDB: 3K4Q) and 3-phytase B (PDB: 1QFX) were characterized using bioinformatic tools. Results showed that both enzymes have highly conserved catalytic pockets, supporting their classification as histidine acid phosphatases. 2D structures consist of 43% alpha-helix, 12% beta-sheet, and 45% others and 38% alpha-helix, 12% beta-sheet, and 50% others, respectively, and pI 4.94 and 4.60, aliphatic index 72.25 and 70.26 and average hydrophobicity of −0,304 and −0.330, respectively, suggesting aqueous media interaction. Glycosylation and glycation sites allowed detecting zones that can affect folding and biological activity, suggesting fragmentation. Docking showed that H59 and H63 act as nucleophiles and that D339 and D319 are proton donor residues. MW of 3K4Q (48.84 kDa) and 1QFX (50.78 kDa) is similar; 1QFX forms homodimers which will originate homotetramers with several catalytic center accessible to the ligand. 3K4Q is less stable (instability index 45.41) than 1QFX (instability index 33.66), but the estimated lifespan for 3K4Q is superior. Van der Waals interactions generate hydrogen bonds between the active center and O2 or H of the phytic acid phosphate groups, providing greater stability to these temporal molecular interactions.

In Silico Study of Secondary Structure of Hemoglobin Protein

2021 ◽  
pp. 6245-6249
Author(s):  
Roma Chandra
Keyword(s):  
Secondary Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Alpha Helix ◽  
Prediction Methods ◽  
Protein Secondary Structures

Protein structure prediction is one of the important goals in the area of bioinformatics and biotechnology. Prediction methods include structure prediction of both secondary and tertiary structures of protein. Protein secondary structure prediction infers knowledge related to presence of helixes, sheets and coils in a polypeptide chain whereas protein tertiary structure prediction infers knowledge related to three dimensional structures of proteins. Protein secondary structures represent the possible motifs or regular expressions represented as patterns that are predicted from primary protein sequence in the form of alpha helix, betastr and and coils. The secondary structure prediction is useful as it infers information related to the structure and function of unknown protein sequence. There are various secondary structure prediction methods used to predict about helixes, sheets and coils. Based on these methods there are various prediction tools under study. This study includes prediction of hemoglobin using various tools. The results produced inferred knowledge with reference to percentage of amino acids participating to produce helices, sheets and coils. PHD and DSC produced the best of the results out of all the tools used.

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