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We investigated the properties of the low molecular weight thermo-alkali-stable and mercury ion-tolerant xylanase production from Thermomyces dupontii KKU-CLD-E2-3. The xylanase was purified to homogeneity by ammonium sulfate, Sephadex G-100 and DEAE-cellulose column chromatography which resulted 27.92-fold purification specific activity of 56.19 U/mg protein and a recovery yield of 2.01%. The purified xylanase showed a molecular weight of 25 kDa by SDS-PAGE and the partial peptide sequence showed maximum sequence homology to the endo-1,4-β-xylanase. The optimum temperature and pH for its activity were 80 °C and pH 9.0, respectively. Furthermore, the purified xylanase can maintain more than 75% of the original activity in pH range of 7.0-10.0 after incubation at 4 °C for 24 h, and can still maintain more than 70% of original activity after incubating at 70 °C for 90 min. Our purified xylanase was activated by Cu 2+ and Hg 2+ up to 277% and 235% of initial activity, respectively but inhibited by Co 2+ , Ag + and SDS at a concentration of 5 mM. The K m and V max values of beechwood xylan were 3.38 mg/mL and 625 µmol/min/mg, respectively. Furthermore, our xylanase had activity specifically to xylan-containing substrates and hydrolyzed beechwood xylan, and the end products mainly were xylotetraose and xylobiose. The results suggested that our purified xylanase has potential to use for pulp bleaching in the pulp and paper industry.

Automatically extracting protein names from the literature and linking these names to the associated entries in sequence databases is becoming increasingly important for annotating biological databases. NLProt is a novel system that combines dictionary- and rule-based filtering with several support vector machines (SVMs) to tag protein names in PubMed abstracts. When considering partially tagged names as errors, NLProt still reached a precision of 75% at a recall of 76%. By many criteria our system outperformed other tagging methods significantly; in particular, it proved very reliable even for novel names. Names encountered particularly frequently in Drosophila, such as white, wing and bizarre, constitute an obvious limitation of NLProt. Our method is available both as an Internet server and as a program for download (http://cubic.bioc.columbia.edu/services/NLProt/). Input can be PubMed/MEDLINE identifiers, authors, titles and journals, as well as collections of abstracts, or entire papers.

A single amino acid in a peptide sequence can play an important role to tune the self‐assembly and hydrogelation behaviour. Here, a C‐terminal cysteine‐containing ultrashort peptide hydrogelator forms hydrogel through non‐covalent and covalent interactions. Interestingly, the hydrogel is insoluble in water and buffer solutions at different pH values (1‐13) and is thixotropic and injectable. In recent years, removing dyes from contaminated water has become a significant concern because of the shortage of freshwater resources. Therefore, the adsorption of dyes through a reliable, straightforward, nontoxic, cheap, and environmentally friendly adsorbent has become a popular topic. Hence, the hydrogelator was exploited to remove organic dyes from wastewater, harnessing its applicability in the gel phase and solid supports (filter paper and cotton). [ABSTRACT FROM AUTHOR]

1. A new method is described for ;fingerprinting' cysteic acid peptides derived from the disulphide bridges of proteins. Cystine peptides are separated by paper electrophoresis and oxidized on paper by performic acid vapour. Electrophoresis at right angles to the first direction produces parallel groups of cysteic acid peptides lying off a diagonal. This ;fingerprint' reveals the way in which the cysteic acid peptides were originally joined in the protein. 2. The method allows a very easy selective purification of cysteic acid peptides. 3. By applying this method to bovine chymotrypsinogen A, we found that the half-cystine residues were linked 1-122, 42-58, 136-201, 168-182 and 191-220.

A novel xylanase gene xynBCA , encoding a polypeptide of 439 residues (XynBCA), was cloned from Caldicoprobacter algeriensis genome and recombinantly expressed in Escherichia coli BL21(DE3). The amino acid sequence analysis showed that XynBCA belongs to the glycoside hydrolase family 10. The purified recombinant enzyme has a monomeric structure of 52 kDa. It is active and stable in a wide range of pH from 3 to 10 with a maximum activity at 6.5. Interestingly, XynBCA was highly thermoactive with an optimum temperature of 80 °C, thermostable with a half-life of 20 min at 80 °C. The specific activity was 117 U mg−1, while the K m and V max were 1.247 mg ml−1, and 114.7 μmol min−1 mg−1, respectively. The investigation of XynBCA in kraft pulp biobleaching experiments showed effectiveness in releasing reducing sugars and chromophores, with best achievements at 100 U g−1 of pulp and 1 h of incubation. The comparative molecular modeling studies with the less thermostable Xylanase B from Clostridium stercorarium , revealed extra charged residues at the surface of XynBCA potentially participating in the formation of intermolecular hydrogen bonds with solvent molecules or generating salt bridges, therefore contributing to the higher thermal stability. [ABSTRACT FROM AUTHOR]

Thermoalkaliphilic GH11 xylanases are largely favored for paper pulp biobleaching process. The present work aimed to comparatively investigate the molecular phylogeny, amino acid sequences, molecular structure, and enzyme–substrate interaction of six thermoalkaliphilic GH11 xylanases from different bacterial species (Oxalobacteraceae bacterium xylanase = ObXyl, Sphingomonas sp. xylanase = SsXyl, Hymenobacter sp. xylanase = HsXyl, Amycolatopsis vastitatis xylanase = AvXyl, Lentzea deserti xylanase = LdXyl, Streptomyces rubellomurinus xylanase = SrXyl). For this purpose, six bacterial thermoalkaliphilic GH11 xylanase sequences derived from unreviewed protein entries of UniProt/TrEMBL database were analyzed for their phylogenetic relationships and sequence similarities. Also, 3D predicted structures of the enzymes were built and computationally validated by different bioinformatics tools. The enzyme–substrate interactions were investigated by molecular docking analysis using various substrates. Phylogenetic analysis showed that six enzymes were grouped into two different clusters: the first cluster included ObXyl, SsXyl, and HsXyl, whereas the second cluster had AvXyl, LdXyl, and SrXyl. Multiple sequence alignment showed that the second cluster xylanases possessed longer N-terminal regions indicating higher thermostability, compared to the first cluster xylanases. The structural analyses showed that six predicted structures were largely conserved. Molecular docking results indicated that binding efficiency to xylotriose, xylotetraose, and xylopentaose was higher in second cluster enzymes than that in first cluster enzymes, exhibiting mostly above -8.0 kCal/mol of binding energy. Arginine in B8 β-strand was commonly involved in substrate interactions in all the second cluster xylanases, different from the first cluster ones. Thus, the present work predicted that the thermoalkaliphilic xylanases in the second cluster might be greater potential candidates for the paper pulp bleaching process. [ABSTRACT FROM AUTHOR]

1, 2-Cyclohexanedione reacts specifically with the guanidino group of arginine or arginine residues at pH 8 to 9 in sodium borate buffer in the temperature range of 25-40 degrees. The single product, N-7, N-8-(1,2-dihydroxycyclohex-1,2-ylene)-L-arginine (DHCH-arginine) is stable in acidic solutions and in borate buffers (pH 8 to 9). DHCH-Arginine is converted to N-7-adipyl-L-arginine by periodate oxidation. The structures of the two compounds were elucidated by chemical and physicochemical means. Arginine or arginyl residues can be regenerated quantitatively from DHCH-arginine by incubation at 37 degrees in hydroxylamine buffer at pH 7.0 FOR 7 TO 8 hours. Analysis of native egg white lysozyme and native as well as oxidized bovine pancreatic RNase, which were treated with cyclohexanedione, showed that only arginine residues were modified. The utility of the method in sequence studies was shown on oxidized bovine pancreatic ribonuclease A. Arginine modification was complete in 2 hours at 35 degrees in borate buffer at pH 9.0 with a 15-fold molar excess of the reagent. The derived peptides showed that tryptic hydrolysis was entirely limited to peptide bonds involving lysine residues, as shown both by two-dimensional peptide patterns and by isolation of the resulting peptides. The stability of DHCH-arginyl residues permits isolation of labeled peptides.

1. Calf lens alpha-crystallin was carboxymethylated with radioactive sodium iodoacetate to label the thiol group. 2. The protein was then digested with trypsin or alternatively fractionated in urea to obtain the acidic (A) chains, which were then digested with trypsin. Either procedure gave two radioactive peptides containing carboxymethylcysteine. 3. These two peptides were closely related: the longer form contained 28 amino acid residues, and the shorter lacked two residues at the N-terminal end of the longer form. 4. The amino acid sequence of the peptides have been determined. 5. No evidence for the presence of more than one cysteine residue/chain was found. 6. The question of the molecular weight of the chains is discussed.

Lysine crotonylation is a newly discovered and reversible posttranslational modification involved in various biological processes, especially metabolism regulation. A total of 5159 lysine crotonylation sites in 2272 protein groups were identified. Twenty-seven motifs were found to be the preferred amino acid sequences for crotonylation sites. Functional annotation analyses revealed that most crotonylated proteins play important roles in metabolic processes and photosynthesis. Bioinformatics analysis suggested that lysine crotonylation preferentially targets a variety of important biological processes, including ribosome, glyoxylate and dicarboxylate metabolism, carbon fixation in photosynthetic organisms, proteasome and the TCA cycle, indicating lysine crotonylation is involved in the common mechanism of metabolic regulation. A protein interaction network analysis revealed that diverse interactions are modulated by protein crotonylation. These results suggest that lysine crotonylation is involved in a variety of biological processes. HSP70 is a crucial protein involved in protecting plant cells and tissues from thermal or abiotic stress responses, and HSP70 protein was found to be crotonylated in paper mulberry. This systematic analysis provides the first comprehensive analysis of lysine crotonylation in paper mulberry and provides important resources for further study on the regulatory mechanism and function of the lysine crotonylated proteome. [ABSTRACT FROM AUTHOR]

The light chain of rabbit immunoglobulin G was shown to contain 15-20% blocked N-terminal residue. The blocked residue is pyrrolid-2-one-5-carboxylic acid, and most of the chains that contain this residue have the N-terminal sequence pyrrolid-2-one-5-carbonyl-valine.