Protein and Peptide Letters - Volume 17, Issue 12, 2010

The analysis of conformations corresponding to continuous amino acid repeat peptides (CARPs) comprising six or more residues in proteins of known three-dimensional structure revealed that alanine, glycine, glutamic acid, proline, valine, histidine, aspartic acid, glutamine and lysine were associated as repeating amino acid residues. Alanine, glycine and histidine CARPs were most common, although the histidine hexapepti Read More

Protein solubility plays a major role for understanding the crystal growth and crystallization process of protein. How to predict the propensity of a protein to be soluble or to form inclusion body is a long but not fairly resolved problem. After choosing almost 10,000 protein sequences from NCBI database and eliminating the sequences with 90% homologous similarity by CD-HIT, 5692 sequences remained. By using Chou's pseudo Read More

Apoptosis is an essential process for controlling tissue homeostasis by regulating a physiological balance between cell proliferation and cell death. The subcellular locations of proteins performing the cell death are determined by mostly independent cellular mechanisms. The regular bioinformatics tools to predict the subcellular locations of such apoptotic proteins do often fail. This work proposes a model for the sorti Read More

LIM Kinase 2 (LIMK2) is a LIM domain-containing protein kinase which regulates actin polymerization thorough phosphorylation of the actin depolymerizing factor cofilin. It is also known to function as a shuttle between the cytoplasm and nucleus in endothelial cells. A basic amino acid-rich motif in LIMK2 was previously identified to be responsible for this shuttling function, as a nucleolar localization signal (NoLS). Here it Read More

[PSI+] phenotype can be transiently induced when Magnesium chloride (MgCl2) was the selective pressure in SUP35 repeat-expansion mutant [psi-] yeast strains. We further investigated [PSI+] phenotype change under different MgCl2 conditions with native Sup35p and quantified the Sup35p status changes with fluorescence recovery after photobleaching (FRAP) and semi-denaturing detergent-agarose gel electrophoresis (SD Read More

Rational drug design is an important step towards effective patient care enabling lead molecule discovery in a relatively faster and inexpensive way. This article describes a variable string length genetic algorithm with domain specific operators for de novo ligand design. The algorithm first mines the active site of the given protein receptor whose geometry and chemical composition guides the ligand building. Active site mined by t Read More

Fowlicidin-3 and fowlicidin-1 are cathelicidin-type antimicrobial peptides found in chicken. They effectively inhibit the proliferation of many gram-positive and gram-negative bacteria. To obtain sufficient amounts of these peptides for possible use in therapeutic applications, DNA encoding each full-length gene, including all exons and introns, was fused to the β-casein promoter in a pBC1 vector that was then introduced into C12 Read More

The interaction between cyclophosphamide monohydrate with human serum albumin (HSA) and human serum transferrin (hTf) was studied with UV absorption, fluorescence and circular dichroism (CD) spectroscopies as well as molecular modeling. Based on the fluorescence quenching results, it was determined that HSA and hTf had two classes of apparent binding constants and binding sites at physiological conditions. Read More

Information about interactions between enzymes and small molecules is important for understanding various metabolic bioprocesses. In this article we applied a majority voting system to predict the interactions between enzymes and small molecules in the metabolic pathways, by combining several classifiers including AdaBoost, Bagging and KNN together. The advantage of such a strategy is based on the principle that a pred Read More

The present paper is an attempt to study the mechanism of ethanol induced aggregation of chicken egg albumin and to stabilize the protein against ethanol induced aggregation. The protein aggregation was determined by monitoring the light scattering of protein aggregates spectrophotometrically. The protein undergoes certain structural changes in water- ethanol solution and the degree of aggregation was Read More

We propose a novel concept associated with the relationship between structure and function in biomolecular systems. We performed a 75 nanoseconds molecular dynamics (MD) simulation for an RNA-binding protein, neurooncological ventral antigen (NOVA), and examined its physico-chemical properties. NOVA dissociated from the NOVARNA complex showed a large conformational change: formation of intra-molecula Read More

Multidrug-resistance-associated protein 6 (MRP6/ABCC6) is a protein belonging to the ABC transporter family. Proteins in this family share many characteristic structural features, including two membrane-spanning domains and two nucleotide-binding domains (NBD1 and NBD2), that function cooperatively but not equally bind and hydrolyze ATP. The MRP6 protein is structurally and functionally poorly characterized. Previously, Read More

Asparagine can be non-enzymatically deamidated and isomerized via succinimide to isoaspartate. This posttranslational modification can potentially alter the physical properties or the function of the parent protein. Asn32 of ribonuclease U2A from Ustilago sphaerogena is known to rapidly deamidate and isomerize in alkaline conditions. The crystal structure of ribonuclease U2A complexed with 2´-adenylic acid and c Read More

Antibody-directed enzyme prodrug therapy (ADEPT) delivers chemotherapeutic agents at high concentration to tumor tissues while minimizing systemic drug exposure. β-Lactamases are particularly useful enzymes for ADEPT systems due to their unique substrate specificity, which allows the activation of a variety of lactam-based prodrugs with minimal interference from mammalian enzymes. This study used integrin αv β Read More

Caspases play an important role in many critical non-apoptosis processes by cleaving relevant substrates at cleavage sites. Identification of caspase substrate cleavage sites is the key to understand these processes. This paper proposes a hybrid method using support vector machine (SVM) in conjunction with position specific scoring matrices (PSSM) for caspase substrate cleavage sites prediction. Three encoding sche Read More