Protein and Peptide Letters - Volume 19, Issue 4, 2012

Many proteins bear multi-locational characteristics, and this phenomenon is closely related to biological function. However, most of the existing methods can only deal with single-location proteins. Therefore, an automatic and reliable ensemble classifier for protein subcellular multi-localization is needed. We propose a new ensemble classifier combining the KNN (K-nearest neighbour) and SVM (support vector machin Read More

Computational prediction of protein structural class based on sequence data remains a challenging problem in current protein science. In this paper, a new feature extraction approach based on relative polypeptide composition is introduced. This approach could take into account the background distribution of a given k-mer under a Markov model of order k-2, and avoid the curse of dimensionality with the increase of Read More

DNA-binding proteins play an important role in most cellular processes, such as gene regulation, recombination, repair, replication, and DNA modification. In this article, an optimal Chou's pseudo amino acid composition (PseAAC) based on physicochemical characters of amino acid is proposed to represent proteins for identifying DNAbinding proteins. Six physicochemical characters of amino acids are utilized to genera Read More

O-Acyl isodipeptides are prepared by coupling Boc-Ser/Thr-OBzl with Fmoc-Xaa-OH employing COMU, well known third generation peptide coupling agent. The reaction proceeds with high yield and the chemical homogeneity of the synthesized molecules were established via chiral HPLC analyses. The O-acyl isodipeptide units play crucial role in the success of ‘ click peptide’ protocol employed for assembling ‘ difficult sequ Read More

Outer membrane proteins (OMPs) play important roles in cell biology. In addition, OMPs are targeted by multiple drugs. The identification of OMPs from genomic sequences and successful prediction of their secondary and tertiary structures is a challenging task due to short membrane-spanning regions with high variation in properties. Therefore, an effective and accurate silico method for discrimination of OMPs from th Read More

A prior knowledge of protein structural class can provide useful information about its overall structure. So, it is vitally important to develop a computational prediction method for fast and accurately determining the protein structural class. In this paper, a dual-layer wavelet support vector machine (WSVM) is presented via the general form of Chou's pseudo amino acid composition, which is featured by introducing wavelet Read More

Defensins are important components in host defense systems. The therapeutic use of β-defensins is limited by their innate toxicity and high cost due to the size and complex disulfide pairing. In this study, we used linear avian β- defensin-4 (RL38) without disulfide bonds as model peptide to derive two peptides by the truncation. GL23 is the Cterminal truncated sequence of RL38, and GLI23 is the derivative of GL23 by the repl Read More

Identification on protein folding types is always based on the 27-class folds dataset, which was provided by Ding & Dubchak in 2001. But with the avalanche of protein sequences, fold data is also expanding, so it will be the inevitable trend to improve the existing dataset and expand more folding types. In this paper, we construct a multi-class protein fold dataset, which contains 3,457 protein chains with sequence identity b Read More

As major chaperone of eye lens, alpha-crystallin (&agr:-Crs) is responsible for the transparency and refractive power of this region by preventing denaturation and precipitation of other proteins. As shown previously, cataract formation was positively associated with high salt intake and the elevation of blood sugar level. Here the effect of both temperature and ionic strength were studied on structure and chaperoning functi Read More

Human antimicrobial peptides (AMPs), including defensins, have come under intense scrutiny owing to their key multiple roles as antimicrobial agents. Not only do they display direct action on microbes, but also recently they have been shown to interact with the immune system to increase antimicrobial activity. Unfortunately, since mechanisms involved in the binding of AMPs to mammalian cells are largely unknown, their p Read More

Measles virus (MV), one of the most contagious agents, infects immune cells using the signaling lymphocyte activation molecule (SLAM) on the cell surface. A complex of SLAM and the attachment protein, hemagglutinin (MVH), has remained elusive due to the intrinsic handling difficulty including glycosylation. Furthermore, crystals obtained of this complex are either nondiffracting or poorly-diffracting. To solve this problem, we de Read More

Bauninia forficata is trivially known as cow paw, and popularly used in Brazil for treatment of diabetes mellitus. Denominated baupain a cysteine proteinase was purified from B. forficata leaves. In this study, we investigated the baupain effect on aggregation of isolated human platelets in vitro and the results show that baupain hinders thrombin - but not ADP- and collagen- induced platelet aggregation. With synthetic quenched- Read More