Protein and Peptide Letters - Volume 17, Issue 9, 2010

We are very pleased to offer this special issue to the readers of Protein and Peptide Letters by selecting the candidate papers from the 2009 International Conference on Intelligent Computing (ICIC), held on September 16-19, 2009 in Ulsan, Korea. Eleven papers representing less than five percent of all eligible papers accepted at the ICIC2009 are selected for inclusion in this special issue. In recent years, we have witnessed Read More

Protein-protein interactions (PPIs) are key components of most cellular processes, so identification of PPIs is at the heart of functional genomics. A number of experimental techniques have been developed to discover the PPI networks of several organisms. However, the accuracy and coverage of these techniques have proven to be limited. Therefore, it is important to develop computational methods to assist in the design and v Read More

Identifying protein-protein interaction is crucial for understanding the biological systems and processes, as well as mutant design. This paper proposes a novel hybrid Genetic Algorithm/Support Vector Machine (GA/SVM) method to predict the interactions between proteins intermediated by the protein-domain relations. A protein domain is a structural and/or functional unit of the protein. Every protein can be characterized b Read More

With a huge amount of protein sequence data, the computational method for protein-protein interaction (PPI) prediction using only the protein sequences information have drawn increasing interest. In this article, we propose a sequence- based method based on a novel representation of local protein sequence descriptors. Local descriptors account for the interactions between residues in both continuous and discontinuou Read More

In the yeast protein-protein interaction network, motif mode, a collection of motifs of special combinations of protein nodes annotated by the molecular function terms of the Gene Ontology, has revealed differences in the conservation constraints within the same topology. In this study, by employing an intelligent agent-based distributed computing method, we are able to discover motif modes in a fast and adaptive manner Read More

In protein-RNA interactions, amino acids often exhibit different preferences for its RNA partners with different neighbor amino acids. Hence, the interaction propensity of an amino acid can be better assessed by considering neighbors of the amino acid than examining the amino acid alone. In this study, we computed the interaction propensity of three consecutive amino acids (called amino acid triplet or triple amino acids) fro Read More

Prediction of protein-protein interaction sites can guide the structural elucidation of protein complexes. We propose a novel method using a radial basis function neural network (RBFNN) ensemble model for the prediction of protein interaction sites in heterocomplexes. We classified protein surface residues into interaction sites or non-interaction sites based on the RBFNNs trained on different datasets, then judged a predicti Read More

π-turns are irregular secondary structure elements consisting of short backbone fragments (six-amino-acid residues) where the backbone reverses its overall direction. They play an important role in proteins from both the structural and functional points of view. Recently, some methods have been proposed to predict π-turns. In this study, a new method of π-turn prediction that uses a two-stage classification scheme is propos Read More

In this study, we propose a new method to predict β-Hairpins in proteins and its evaluation based on the support vector machine. Different from previous methods, new feature representation scheme based on auto covariance is adopted. We also investigate two structure properties of proteins (protein secondary structure and residue conformation propensity), and examine their effects on prediction. Moreover, we emp Read More

Peptide fragments that serve as the cytotoxic T lymphocyte (CTL) epitopes are processed from antigens by the proteasome and then are transported to the endoplasmic reticulum through transporter associated with antigen processing (TAP) before being loaded onto the MHC class I molecule. Here, we studied TAP specificity by a neighborhood rough set (NRS) model based feature selection and prioritization method. Read More

A weighted sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. Weighted sequences are able to summarize poorly defined short sequences, as well as the profiles of protein families and complete chromosome sequences. Thus it is of biological and theoretical significance to design powerful algorithms on weighted sequences. A common task is to identify re Read More

A computational model is introduced for predicting peptide drift time in ion mobility-mass spectrometry (IMMS). Each peptide was represented using a numeric descriptor: molecular weight. A simple linear regression predictor was constructed for peptides drift time prediction. Three datasets with different charge state assignments were used for the model training and testing. The dataset one contains 212 singly char Read More

A Surface Plasmon Resonance Imaging (SPRI) sensor has been developed for highly selective determination of cathepsin D (Cat D) or/and E (Cat E). The sensor contains immobilised pepstatin A, which binds aspartyl proteases from solution. Pepstatin A activated with N-Hydroxysuccinimide (NHS) and N-Ethyl-N'-(3-dimethylaminopropyl) carbodiimide (EDC) was immobilized on an amine-modified gold surface. Cysteamine was used f Read More

The lens protein, γB-crystallin, precipitates during cataract formation. As a recombinant protein, in aqueous solution, γB aggregates and precipitates upon heating, cooling, exposure to ultraviolet light, or refolding from a denatured state. We have studied soluble γB crystallin, as well as each of the above aggregated forms, to determine whether γB's polypeptide chain is differently organized in each form. For this purp Read More

It has generally been accepted that an increase in protein stability is proportional to the increase in hydrophobicity. When a cavity is created by large-to-small substitutions of amino acid residues in protein cores, protein stability decreases 5.3 kJ/mol per single methyl(ene) group removal. In contrast, many reported cavity-filling mutations either failed to increase stability or produced marginal increases in stability; even in suc Read More

Bla g 6, a German cockroach allergen, shows homology to muscle protein troponin C. It contains four calcium-binding domains at 20-30, 56-67, 96-107, and 132-143 amino acid (aa) residues, and its immunoglobulin E (IgE) reactivity is dependent upon calcium ion level. However, the IgE binding epitopes of Bla g 6 have not been investigated. This study aimed to analyze the IgE binding epitopes from the five peptide fragments of Read More

There is a growing body of evidence that the formation and accumulation of advanced glycation end products (AGE) have been known to progress under diabetic conditions, thereby being involved in diabetic vascular complications. Further, we, along with others, have recently found AGE could disturb insulin actions in cultured adipocytes and skeletal muscles. However, the pathological role of AGE in insulin resistance in vivo is n Read More