Protein and Peptide Letters - Volume 18, Issue 9, 2011

CTX-M-15, an extended-spectrum β-lactamase emerging worldwide, hydrolyzes lactam ring of β-lactam antibiotics, and thus causes therapeutic failure and a lack of eradication of pathogenic bacteria by third-generation β-lactams. Therefore, the enzyme is a potential target for developing agents against pathogens isolated from patients suffering from nosocomial infections. The CTX-M-15 protein was purified and crystallize Read More

AcrB is an inner membrane protein in Escherichia coli that is a component of a triplex AcrA-AcrB-TolC (AcrAB- TolC) multidrug efflux pump. The AcrAB-TolC complex and its homologues are highly conserved among Gramnegative bacteria and are major players in conferring multidrug resistance (MDR) in many pathogens. In this study we developed a disulfide trapping method that may reveal AcrB conformational chan Read More

G-protein coupled receptor (GPCR) is a protein family that is found only in the Eukaryotes. They are used for the interfacing of cell to the outside world and are involved in many physiological processes. Their role in drug development is evident. Hence, the prediction of GPCRs is very much demanding. Because of the unavailability of 3D structures of most of the GPCRs, the statistical and machine learning based prediction of Read More

Catalase is an enzyme that occurs in almost all aerobic organisms. Its main metabolic function is to prevent oxidative damage to tissues induced by hydrogen peroxide which is a strong oxidizing agent. Catalase is very effective in performing this task, since it has the highest turnover rate among all the enzymes. The properties of catalase have been investigated extensively for many years; however, the role of the solvent molecul Read More

In the biomimetic design two hydrophobic pentapetides Boc-Ile-Aib-Leu-Phe-Ala-OMe (I) and Boc-Gly-Ile- Aib-Leu-Phe-OMe (II) (Aib: α-aminoisobutyric acid) containing one Aib each are found to undergo solvent assisted selfassembly in methanol/water to form vesicular structures, which can be disrupted by simple addition of acid. The nanovesicles are found to encapsulate dye molecules that can be released by the Read More

Protein-protein interaction hot spots, as revealed by alanine scanning mutagenesis, make dominant contributions to the free energy of binding. Since mutagenesis experiments are expensive and time-consuming, the development of computational methods to identify hot spots is becoming increasingly important. In this study, by using a new combination of sequence, structure and energy features, we propose an iterative s Read More

Protein-protein interactions (PPIs) are crucial to most biochemical processes in human beings. Although many human PPIs have been identified by experiments, the number is still limited compared to the available protein sequences of human organisms. Recently, many computational methods have been proposed to facilitate the recognition of novel human PPIs. However the existing methods only concentrated on the informati Read More

Hypoxia caused by waterlogging results in a severe loss of crop production. At the primary stage of wheat development, the seminal roots have strategies to survive under hypoxia through alternative metabolism coupling root anatomical modification. The present study used a model system of lysigenous aerenchymatous seminal roots from a representative seedling stage of wheat to elucidate the root physiology in response Read More

One of the main challenges faced by biological applications is to predict protein subcellular localization in automatic fashion accurately. To achieve this in these applications, a wide variety of machine learning methods have been proposed in recent years. Most of them focus on finding the optimal classification scheme and less of them take the simplifying the complexity of biological systems into account. Traditionally, such Read More

Separate and simultaneous binding effects of paclitaxel (a drug with anti-tumor activity) and estradiol (used for treating multiple maladies) with human serum albumin (HSA) were investigated by fluorescence quenching, UV absorption, circular dichroism, zeta potential and molecular dynamic techniques. An extensive fluorescence quenching was observed during the reaction of drugs and HSA and was rationalized in t Read More

Two arginine side-chain protecting groups, NG-4-methoxy-2,3,6-trimethylbenzensulfonyl group (Mtr) and NG- 2,2,5,7,8-pentamethylchroman-6-sulfonyl (Pmc), have been investigated at both the Arg1 and/or Arg9 position of the bioactive peptide, Bradykinin using Fluorenylmethyloxycarbonyl (Fmoc) Solid Phase Peptide Synthesis. A more efficient synthesis of the peptide has been found when a combination of Arg(Mtr) is prese Read More

MHC-epitope binding plays a key role in the cellular immune response. Accurate prediction of MHC-epitope binding affinity can greatly expedite epitope screening by reducing costs and experimental effort. In this paper, 13 T descriptors, which derived from 544 physicochemical properties of the natural amino acids, were used to characterize 4 MHC class I alleles epitope peptide sequences, the optimal QSAR models were con Read More