Protein and Peptide Letters - Volume 16, Issue 12, 2009

This issue of Protein and Peptide Letters is the second one in which all the manuscripts have been contributed by members of the Editorial Advisory Board, following an earlier issue last year (Vol. 15 No. 9, 2008). The papers included here demonstrate the wide variety of research areas covered by the Editorial Board. The field of proteins and peptides is very broad, encompassing wide areas of current chemistry, biology, biomaterials and related areas. This is true, of course, because protein and peptides can be found in all living systems and are responsible for both form and function, i.e., structural proteins and enzymes, to name just two examples. The accelerating discoveries of the roles of these molecules in the pathology of diseases and in new biomaterials with useful properties promise to expand the field even further. Now that we have expanded the publication of Protein & Peptide Letters to 12 issues per year, we plan to continue scheduling the December issue each year for papers submitted by Editorial Advisory Board members. Each manuscript is submitted to the Editor-in-Chief and subjected to the same peer review process as all other submissions to the journal. We invite our EABMs to begin planning for submission of their best work for the December 2010 issue. It is also a pleasure to announce that the Content Management System for online submission of abstracts and manuscript is now fully functional. All authors are invited to access the system at http://www.bentham-editorial.org to register and submit your documents. Follow the online prompts to establish a username and password and then you can access your manuscript and read comments from the referees.

In this work, we present an advanced fluorescence assay for the detection of traces of ocratoxin A and neomycin in food. The described assay is based on measurement of the fluctuations of the fluorescein-labeled analytes by a focused laser beam in the absence and in the presence of the specific antibodies anti-analytes. A competitive assay based on the utilization of unlabeled analytes was developed. The obtained results indicated that the combination of high-avidity IgG antibodies together with an innovative fluorescence immunoassay strategy resulted in the detection limit of 0.0078 ng and 0.0156 ng for ochratoxin A and neomycin, respectively.

Piper tuberculatum is an exotic Piper from the Amazon region that shows resistance to infection by Fusarium solani f. sp. piperis, causal agent of Fusarium disease in black pepper (Piper nigrum L.). In this work we aimed to study the interaction between P. tuberculatum and F. solani f. sp. piperis at a molecular level, using suppression subtractive hybridization to identify genes potentially related to Fusarium disease resistance. Comparative sequence analysis confirmed that clones isolated here show a high identity with genes coding for proteins that have a known role in plant defense response mechanisms, such as peroxidase, hydroxyproline-rich glycoprotein and CBL-interacting protein kinase. The present study constitutes the first effort to understand the molecular basis of this plant-pathogen interaction, identifying genes which may be used in the future genetic improvement of black pepper.

A novel endo-α-L-arabinanase gene (arn2) was isolated, and expressed in E. coli in active form. The recombinant enzyme (ARN2) had optimum activity at pH 6.0 and 45-50oC with stability between pH 5.0-8.0 and at temperatures up to 40oC. The recombinant ARN2 catalyzed internal cleavage of α-1,5 glycosidic bonds of CM-arabinan, debranched arabinan, linear arabinan, and sugar beet (native) arabinan at rates of decreasing order, and was inactive on wheat arabinoxylan and p-nitrophenyl- α-L-arabinofuranoside. Kinetic analysis showed that branching in the arabinan did not significantly affect the apparent Km values, and the difference in the reaction rates was likely due to the chemical step after substrate binding. The enzyme hydrolyzed arabino-oligosaccharides of DP 6 to smaller oligomers and mostly arabinotriose. Natural and modified arabinans were cleaved to oligomers of various chain lengths, which were progressively hydrolyzed to yield arabinotriose. The pattern of degradation revealed an endo-acting mechanism with arabinotriose as the end product.

Mutations in the LRRK2 gene have been implicated in the pathogenesis of Parkinson's disease. This work provides biochemical evidence that the ROC domain of LRRK2 functions as a small GTPase, and the Parkinson's disease-associated mutants do not appear to have reduced GTP hydrolysis activities.

B-factor is highly correlated with protein internal motion, which is used to measure the uncertainty in the position of an atom within a crystal structure. Although the rapid progress of structural biology in recent years makes more accurate protein structures available than ever, with the avalanche of new protein sequences emerging during the post-genomic Era, the gap between the known protein sequences and the known protein structures becomes wider and wider. It is urgent to develop automated methods to predict B-factor profile from the amino acid sequences directly, so as to be able to timely utilize them for basic research. In this article, we propose a novel approach, called PredBF, to predict the real value of B-factor. We firstly extract both global and local features from the protein sequences as well as their evolution information, then the random forests feature selection is applied to rank their importance and the most important features are inputted to a two-stage support vector regression (SVR) for prediction, where the initial predicted outputs from the 1st SVR are further inputted to the 2nd layer SVR for final refinement. Our results have revealed that a systematic analysis of the importance of different features makes us have deep insights into the different contributions of features and is very necessary for developing effective B-factor prediction tools. The two-layer SVR prediction model designed in this study further enhanced the robustness of predicting the B-factor profile. As a web server, PredBF is freely available at: http://www.csbio.sjtu.edu.cn/bioinf/PredBF for academic use.

Aurein 2.5 (GLFDIVKKVVGAFGSL-NH2) is an amphibian antimicrobial peptide. Here, characterisation studies showed the peptide to exhibit molecular areas at an air / water interface (1.77 - 3.1 nm2), which are in agreement with the adoption of α-helical structures. Lipid monolayer studies showed aurein 2.5 to induce maximal surface pressure changes of circa 7 mN m-1 in monolayers formed from phosphatidylglycerol (PG) and circa 6 mN m-1 in those formed from phosphatidylethanolamine (PE). These data indicate that the membrane interactions of the peptide are amphiphilicity driven with no apparent electrostatic requirement. Individually mutating the phenylalanine residues of aurein 2.5 to leucine had no major effect on the levels of PG and PE interactions, suggesting that these residues are not essential to the membrane interactions of the peptide, contrasting to other aureins where corresponding phenylalanine residues are required for efficient membrane interaction and antibacterial activity. This difference in the requirement is suggested to relate to the surface architecture as proposed by the concept of the molecular perturbation potential.

DrTI was effective against trypsin-like enzymes from A. kuehniella and C. cephalonica, however an artificial diet was insufficient to affect the survival and body weight of either insect. The inhibitor stimulated chymotrypsin-like enzymes and probably induced the synthesis of enzymes insensitive to TLCK in neonate larvae.

A series of Val-Leu based peptidic aldehydes containing either a furan or thiophene at the Nterminus was prepared and assayed against ovine m-calpain. In general, potency is favoured by a 2- substituted (rather than 3-substituted) heterocycle, a thiophene rather than a furan, and a shorter chain length at the N-terminus. Molecular docking experiments provide some rationale for these observations.

Bucain, a potent neurotoxin isolated from the venom of the Malayan krait (Bungarus candidus), induces paralysis and death. Its crystal structure has been determined at 2.10 A resolution and based on the molecular topology and hydrophobicity profile is structurally classified as a three-fingered α-neurotoxin possessing a positively charged AChR-binding site.

In this paper, a new predictor called “Gpos-mPLoc”, is developed for identifying the subcellular localization of Gram positive bacterial proteins by fusing the information of gene ontology, as well as the functional domain information and sequential evolution information. Compared with the old Gpos-PLoc, the new predictor is much more powerful and flexible. Particularly, it also has the capacity to deal with multiple-location proteins as indicated by the character “m” in front of “PLoc” of its name. For a newlyconstructed stringent benchmark dataset in which none of included proteins has ≥ 25% pairwise sequence identity to any other in a same subset (location), the overall jackknife success rate achieved by Gpos-mPLoc was 82.2%, which was about 10% higher than the corresponding rate by the Gpos-PLoc. As a user friendly web-server, Gpos-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/Gpos-multi/.

Curcumin is a natural product with diverse pharmacological activities. Studies of curcumin and its structural derivatives have been a subject of growing interest as a result of their diverse biological activities. We report the interaction of diacetylcurcumin (DAC) with Ribonuclease A (RNase A). The binding constant of DAC with RNase A was found to be of the order of 104 M-1. The intrinsic fluorescence of RNase A was quenched by DAC with a quenching constant of 2.2 x 104 M-1. The distance between the fluorophore of RNase A and DAC was found to be 2.6 nm, calculated from a Förster type fluorescence resonance energy transfer (FRET). Secondary structural changes of RNase A after binding were analyzed from circular dichroism and Fourier transform infrared studies. Protein-ligand docking studies were conducted to determine the residues involved in the interaction of RNase A with DAC and changes in the accessible surface of the interacting residues were calculated accordingly.

The 1H NMR Fast Field Cycling relaxometry was applied to study the molecular dynamics of the human protein HC (α1-microglobulin), its hydration and aggregation in solution state. The 1H NMRD data have revealed the complex nature of the water/protein HC system resulting from the co-existence of monomer and dimer forms of the protein in solution as well as the presence of oligosaccharides linked to the polypeptide chain. A comparison of the average correlation time values <ζc> obtained from the model-free fits with the values predicted on the basis of hydrodynamic ζr theory, suggests that the dynamics in solution state is governed mainly by the dimer form of the protein HC (the dominant contribution to the water proton-spin lattice relaxation comes from exchanging protons from the surface of the dimer). The existence of small number of oligomeric forms of the protein HC in solutions is postulated because of the two-step shape of water proton spin-lattice relaxation rate dispersion profiles.

The gastrointestinal peptide hormone gastrin is responsible for initiating the release of gastric acid in the stomach in response to the presence of food and/or humoral factors such as gastrin releasing peptide. However, it has a role in the growth and maintenance of the gastric epithelium, and has been implicated in the formation and growth of gastric cancers. Hypergastrinemia resulting from atrophic gastritis and pernicious anemia leads to hyperplasia and carcinoid formation in rats, and contributes to tumor formation in humans. Additionally, gastrin has been suspected to play a role in the formation and growth of cancers of the colon, but recent studies have instead implicated gastrin processing intermediates, such as gastrin-17-Gly, acting upon a putative, non-cholecystokinin receptor. This review summarizes the production and chemical structures of gastrin and of the processing intermediate gastrin-17-Gly, as well as their activities in the gastrointestinal tract, particularly the promotion of colon cancers.

To test the hypothesis that the ability to form ordered β-rich amyloid fibers with identical structures is a generic property of proteins we present a study on the overall structures of fibers formed by apomyoglobin mutants that either stabilize or destabilize the native state or the intermediate. Our results indicate that, at least at the macroscopic level, ordered β-rich amyloid fibers have similar structures.

Two trypsin inhibitors (called PdKI-3.1 and PdKI-3.2) were purified from the seeds of the Pithecellobium dumosum tree. Inhibitors were obtained by TCA precipitation, affinity chromatography on Trypsin- Sepharose and reversed-phase-HPLC. SDS-PAGE analysis with or without reducing agent showed that they are a single polypeptide chain, and MALDI-TOF analysis determined molecular masses of 19696.96 and 19696.36 Da, respectively. The N-terminal sequence of both inhibitors showed strong identity to the Kunitz family trypsin inhibitors. They were stable over a wide pH (2-9) and temperature (37 to 100 oC) range. These inhibitors reduced over 84% of trypsin activity with inhibition constant (Ki) of 4.20 x 10-8 and 2.88 x 10-8 M, and also moderately inhibited papain activity, a cysteine proteinase. PdKI-3.1 and PdKI-3.2 mainly inhibited digestive enzymes from Plodia interpunctella, Zabrotes subfasciatus and Ceratitis capitata guts. Results show that both inhibitors are members of the Kunitzinhibitor family and that they affect the digestive enzyme larvae of diverse orders, indicating a potential insect antifeedant.

Intrinsically disordered proteins (IDPs) constitute a recently recognized realm of atypical biologically active proteins that lack stable structure under physiological conditions, but are commonly involved in such crucial cellular processes as regulation, recognition, signaling and control. IDPs are very common among proteins associated with various diseases. Recently, we performed a systematic bioinformatics analysis of the human diseasome, a network that linked the human disease phenome (which includes all the human genetic diseases) with the human disease genome (which contains all the disease-related genes) (Goh, K. I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., and Barabasi, A. L. (2007). The human disease network. Proc. Natl. Acad. Sci. U.S.A. 104, 8685-90). The analysis of this diseasome revealed that IDPs are abundant in proteins linked to human genetic diseases, and that different genetic disease classes varied dramatically in the IDP content (Midic U., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2009) Protein disorder in the human diseasome: Unfoldomics of human genetic diseases. BMC Genomics. In press). Furthermore, many of the genetic diseaserelated proteins were shown to contain at least one molecular recognition feature, which is a relatively short loosely structured protein region within a mostly disordered segment with the feature gaining structure upon binding to a partner. Finally, alternative splicing was shown to be abundant among the diseasome genes. Based on these observations the humangenetic- disease-associated unfoldome was created. This minireview describes several illustrative examples of ordered and intrinsically disordered members of the human diseasome.

The potential of human glucagon-like peptide-1 (hGLP-1) as a therapeutic agent is limited by its high aggregation propensity. We show that hGLP-1 forms amyloid-like structures that are preceded by cytotoxic aggregates, suggesting that aggregation of biopharmaceuticals could present a cytotoxic risk to patients besides the reported increased risk in immunogenicity.

Some proteins exhibit characteristics that suggest they have a primary, if not an exclusive role in nutrient reserve storage. The best studied examples are the storage proteins that accumulate specifically in developing seeds. Some of these protein demonstrate biological activities that could contribute to resistance to pest, pathogens or abiotic stresses. In this study we present the biochemical characterization and cloning of the major protein from seeds of T. esculenta (Talisin), a member of the Sapindaceae family. The N-terminal sequence of the protein isolated was used to produce a degenerated primer. This primer allowed the amplification of the Talisin cDNA by RTPCR from mRNA of the T. esculenta seeds protein. The sequence analysis of the cloned cDNA, demonstrated a 756 bp sequence encoding a peptide of 198 amino acids. The deduced peptide presented high similarity to a typical VSP, the 22- kDa protein in lychee (73 %) and 50.0 % identity to Theobroma bicolor reserve protein. Identities of 52.0 % and 44.0 % to trypsin inhibitors from Treobroma mammosum and Populus tremula respectively. In conclusion, we may suggest that Talisin could be a seed storage protein with affinity properties, i.e. interacts with carbohydrates and trypsin enzyme.