scholarly journals Completion of the amino acid sequence of papain

1969 ◽  
Vol 114 (2) ◽  
pp. 279-288 ◽  
Author(s):  
S. S. Husain ◽  
G. Lowe
Keyword(s):  
Acetic Acid ◽  
Amino Acid ◽  
Hydrochloric Acid ◽  
Amino Acid Sequence ◽  
Tertiary Structure ◽  
Primary Sequence ◽  
Inhibited Enzyme

Papain was inhibited with bromo[2−14C]acetic acid, the tertiary structure of the inhibited enzyme was unfolded and the disulphide bridges were reduced with mercaptoethanol and aminoethylated. Digestion with trypsin gave a radioactive peptide consisting of residues 18–58 inclusive and containing therefore the sequence of the thirteen unknown residues 29–41 in the primary sequence of papain. This peptide was digested with pepsin to give a radioactive peptide consisting of residues 18–47, which after digestion with 0·4m-hydrochloric acid gave a radioactive peptide consisting of residues 24–43 inclusive. Further digestion with 6m-hydrochloric acid gave peptides that were used to determine the sequence: Ser-Ala-Val-Val-Thr-Ile-Glx-Gly-Ile-Ile-Lys-Ile-Arg for the residues 29–41, so completing the amino acid sequence of papain.

scholarly journals Catalytic and Molecular Properties of the Quinohemoprotein Tetrahydrofurfuryl Alcohol Dehydrogenase from Ralstonia eutropha Strain Bo

2001 ◽  
Vol 183 (6) ◽  
pp. 1954-1960 ◽  
Author(s):  
Grit Zarnt ◽  
Thomas Schräder ◽  
Jan R. Andreesen
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Alcohol Dehydrogenase ◽  
Tertiary Structure ◽  
Ralstonia Eutropha ◽  
Signal Sequence ◽  
Substrate Inhibition ◽  
Catalytic Efficiency ◽  
Gene Encoding

ABSTRACT The quinohemoprotein tetrahydrofurfuryl alcohol dehydrogenase (THFA-DH) from Ralstonia eutropha strain Bo was investigated for its catalytic properties. The apparentk cat/Km andK i values for several substrates were determined using ferricyanide as an artificial electron acceptor. The highest catalytic efficiency was obtained with n-pentanol exhibiting a k cat/Km value of 788 × 104 M−1 s−1. The enzyme showed substrate inhibition kinetics for most of the alcohols and aldehydes investigated. A stereoselective oxidation of chiral alcohols with a varying enantiomeric preference was observed. Initial rate studies using ethanol and acetaldehyde as substrates revealed that a ping-pong mechanism can be assumed for in vitro catalysis of THFA-DH. The gene encoding THFA-DH from R. eutropha strain Bo (tfaA) has been cloned and sequenced. The derived amino acid sequence showed an identity of up to 67% to the sequence of various quinoprotein and quinohemoprotein dehydrogenases. A comparison of the deduced sequence with the N-terminal amino acid sequence previously determined by Edman degradation analysis suggested the presence of a signal sequence of 27 residues. The primary structure of TfaA indicated that the protein has a tertiary structure quite similar to those of other quinoprotein dehydrogenases.

scholarly journals A DyP-Type Peroxidase of Pleurotus sapidus with Alkene Cleaving Activity

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1536
Author(s):  
Nina-Katharina Krahe ◽  
Ralf G. Berger ◽  
Franziska Ersoy
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Peroxidase Activity ◽  
Tertiary Structure ◽  
Sulphonic Acid ◽  
Anthraquinone Dyes ◽  
Cleavage Activity ◽  
Pleurotus Sapidus ◽  
Β Carotene

Alkene cleavage is a possibility to generate aldehydes with olfactory properties for the fragrance and flavor industry. A dye-decolorizing peroxidase (DyP) of the basidiomycete Pleurotus sapidus (PsaPOX) cleaved the aryl alkene trans-anethole. The PsaPOX was semi-purified from the mycelium via FPLC, and the corresponding gene was identified. The amino acid sequence as well as the predicted tertiary structure showed typical characteristics of DyPs as well as a non-canonical Mn2+-oxidation site on its surface. The gene was expressed in Komagataella pfaffii GS115 yielding activities up to 142 U/L using 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) as substrate. PsaPOX exhibited optima at pH 3.5 and 40 °C and showed highest peroxidase activity in the presence of 100 µM H2O2 and 25 mM Mn2+. PsaPOX lacked the typical activity of DyPs towards anthraquinone dyes, but oxidized Mn2+ to Mn3+. In addition, bleaching of β-carotene and annatto was observed. Biotransformation experiments verified the alkene cleavage activity towards the aryl alkenes (E)-methyl isoeugenol, α-methylstyrene, and trans-anethole, which was increased almost twofold in the presence of Mn2+. The resultant aldehydes are olfactants used in the fragrance and flavor industry. PsaPOX is the first described DyP with alkene cleavage activity towards aryl alkenes and showed potential as biocatalyst for flavor production.

Protein tertiary structure prediction using hidden Markov model based on lattice

2019 ◽  
Vol 17 (02) ◽  
pp. 1950007
Author(s):  
Farzad Peyravi ◽  
Alimohammad Latif ◽  
Seyed Mohammad Moshtaghioun
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Hidden Markov ◽  
Face Centered Cubic ◽  
Tertiary Structure Prediction ◽  
Cubic Lattices ◽  
Face Centered ◽  
Protein Tertiary Structure Prediction

The prediction of protein structure from its amino acid sequence is one of the most prominent problems in computational biology. The biological function of a protein depends on its tertiary structure which is determined by its amino acid sequence via the process of protein folding. We propose a novel fold recognition method for protein tertiary structure prediction based on a hidden Markov model and 3D coordinates of amino acid residues. The method introduces states based on the basis vectors in Bravais cubic lattices to learn the path of amino acids of the proteins of each fold. Three hidden Markov models are considered based on simple cubic, body-centered cubic (BCC) and face-centered cubic (FCC) lattices. A 10-fold cross validation was performed on a set of 42 fold SCOP dataset. The proposed composite methodology is compared to fold recognition methods which have HMM as base of their algorithms having approaches on only amino acid sequence or secondary structure. The accuracy of proposed model based on face-centered cubic lattices is quite better in comparison with SAM, 3-HMM optimized and Markov chain optimized in overall experiment. The huge data of 3D space help the model to have greater performance in comparison to methods which use only primary structures or only secondary structures.

Effects of glacial acetic acid on the extraction, chemical stability, and biological activities of β-LPH

1970 ◽  
Vol 48 (4) ◽  
pp. 511-516 ◽  
Author(s):  
M. Chrétien ◽  
C. Gilardeau
Keyword(s):  
Acetic Acid ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Chemical Stability ◽  
Glacial Acetic Acid ◽  
Biological Activities ◽  
Purification Procedure ◽  
Complete Amino Acid Sequence ◽  
Melanophore Stimulating Hormone ◽  
Stimulating Hormone

Sheep β-lipotropic hormone (β-LPH) contains within its structure the complete amino acid sequence of γ-LPH. These two molecules have a sequence of amino acid entirely similar to βSer-melanophore-stimulating hormone (MSH). We have shown that β-LPH is not likely to be degraded into γ-LPH and β-MSH during the purification procedure, or by incubation in an acetic acid/acetone mixture at 50 °C for 20 min. Results are compatible with the hypothesis that β-LPH could be the biological precursor of β-MSH and that γ-LPH is an intermediate component.

Synopses from the poster exhibition organized by I. M. Kerr, 1. Interferon: a tertiary structure predicted from amino acid sequences

1982 ◽  
Vol 299 (1094) ◽  
pp. 125-127 ◽  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Functional Studies

Functional studies on interferon would be helped by a three-dimensional structure for the molecule. However, it may be several years before the structure of the protein is determined by X-ray crystallography. We have therefore used available methods for predicting the secondary - and the tertiary - structure of a protein from its amino acid sequence to propose a tertiary model involving the packing of four a-helices. Details of this work have been published elsewhere (Sternberg & Cohen 1982).

NEAT-FLEX: Predicting the conformational flexibility of amino acids using neuroevolution of augmenting topologies

2017 ◽  
Vol 15 (03) ◽  
pp. 1750009 ◽  
Author(s):  
Bruno Grisci ◽  
Márcio Dorn
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Tertiary Structure ◽  
Structural Information ◽  
Protein Structures ◽  
Three Dimensional ◽  
Conformational Flexibility ◽  
Amino Acid Sequences ◽  
Conformational Search ◽  
Back Propagation Algorithm

The development of computational methods to accurately model three-dimensional protein structures from sequences of amino acid residues is becoming increasingly important to the structural biology field. This paper addresses the challenge of predicting the tertiary structure of a given amino acid sequence, which has been reported to belong to the NP-Complete class of problems. We present a new method, namely NEAT–FLEX, based on NeuroEvolution of Augmenting Topologies (NEAT) to extract structural features from (ABS) proteins that are determined experimentally. The proposed method manipulates structural information from the Protein Data Bank (PDB) and predicts the conformational flexibility (FLEX) of residues of a target amino acid sequence. This information may be used in three-dimensional structure prediction approaches as a way to reduce the conformational search space. The proposed method was tested with 24 different amino acid sequences. Evolving neural networks were compared against a traditional error back-propagation algorithm; results show that the proposed method is a powerful way to extract and represent structural information from protein molecules that are determined experimentally.

scholarly journals Separation and characterization of the two Asn-linked glycosylation sites of chicken serum riboflavin-binding protein. Glycosylation differences despite similarity of primary structure

1992 ◽  
Vol 285 (1) ◽  
pp. 275-280 ◽  
Author(s):  
J S Rohrer ◽  
H B White
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Primary Structure ◽  
Tertiary Structure ◽  
Binding Protein ◽  
Attachment Site ◽  
Reversed Phase ◽  
Exchange Chromatography ◽  
Protein Glycosylation ◽  
Oligosaccharide Structure

Serum riboflavin-binding protein, a phosphoglycoprotein from the blood of laying hens, contains two Asn-Xaa-(Thr)Ser sequons in very similar but well-separated regions of amino acid sequence. In order to evaluate the effect of local amino acid sequence on the structure of the attached oligosaccharides, serum riboflavin-binding protein was purified to homogeneity, reduced and alkylated, digested with trypsin, and the two glycopeptides were separated by reversed-phase chromatography. After digestion with peptide-N-glycosidase F the released oligosaccharides were separated by high-pH anion-exchange chromatography and the oligosaccharide profiles of the two glycopeptides were compared. Although the two asparagine residues that are glycosylated are contained in pentapeptide segments in which four out of five amino acids are identical, the array of oligosaccharides present at each site show differences in both type and distribution. This suggests that local secondary or tertiary structure, or the order of glycosylation, influences the oligosaccharide structure more than does the primary structure flanking the attachment site.

Site interdependence attributed to tertiary structure in amino acid sequence evolution

Gene ◽  
2005 ◽  
Vol 347 (2) ◽  
pp. 207-217 ◽  
Author(s):  
Nicolas Rodrigue ◽  
Nicolas Lartillot ◽  
David Bryant ◽  
Hervé Philippe
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Tertiary Structure ◽  
Sequence Evolution
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