Protein and Peptide Letters - Volume 17, Issue 4, 2010

We used a de novo designed, β-hairpin forming T1 peptide as a model to investigate the kinetics of peptide fibrogenesis by a combination of light scattering (LS), circular dichroism (CD), fluorescence, and atomic force microscopy (AFM). The results demonstrate that the T1 fibrogenesis undergoes a consecutive stepwise process, with a high degree of cooperation, presenting sigmoidal time-courses of the peptide aggreg Read More

To investigate the processing of transforming growth factor β1 (TGFβ1) pro-protein by furin protease we expressed a GST-pro-TGFβ1 fusion protein in bacteria. Analysis of the furin digestion pattern revealed the liberation of 12.5 kDa TGFβ1 monomers. There was no evidence for cleavage of an alternative furin site within the pro-protein.

Dynamic kinetic resolution (DKR) was demonstrated in the carbodiimide-mediated couplings of N-benzoyl-DLamino acids with L-amino acid esters: the yields of the D-L-peptides significantly exceeded 50% in some cases. NBenzoyl- DL-t-leucine afforded the D-L-peptide almost exclusively (up to 96% yield) in the reaction with methyl Lprolinate, which is the most efficient DKR obtained in the field of amino acids and derivatives.

X-ray crystallography is the most widely used method for protein 3-dimensional structure determination. Selection of target protein that can yield high quality crystal for X-ray crystallography is a challenging task. Prediction of protein crystallization propensity from sequence information is useful for the selection of target protein for crystallization. Recently, support vector machines have been widely used to solve various bi Read More

In insects numerous physiological processes are regulated by neuropeptides. Two fluorescent analogues of the amino acids tryptophan and tyrosine were synthesized and incorporated in the diuretic neuropeptide helicokinin I from the moth Heliothis zea. By fluorescence emission measurements it was shown that both fluorescent helicokinin I analogues react sensitive on the dielectricity of their microenvironment. A helicokinin I a Read More

The stereochemistry of the hydride transfer in reactions catalyzed by NAD(H)-dependent alcohol dehydrogenase from Thermus thermophilus HB27 was determined by means of 1H-NMR spectroscopy. The enzyme transfers the pro-S hydrogen of [4R-2H]NADH and exhibits Prelog specificity. Enzyme-substrate docking calculations provided structural details about the enantioselectivity of this thermophilic enzyme. These results Read More

Most common methods for isolation of the light-harvesting 2 (LH2) complex are time-consuming. In our present work, functional LH2 complex was one-step purified from Rhodobacter sphaeroides by immobilized metal-ion affinity chromatography. The purified LH2 complex exhibited high activity in light absorption and energy transfer. Our present work provides an efficient approach for preparation of functional LH2 complex.

Purpose: A number of proteome studies have been performed recently to identify pheromone-related protein expression and their molecular function using genetically modified rodents' urine. However, no such studies have used Indian commensal rodents; interestingly, in a previous investigation, we confirmed the presence of volatile molecules in commensal rodents urine and these molecules seem to be actively inv Read More

We report that the addition of amino acids to the amyloid peptide dramatically affected the structure and the rate of formation of amyloid fibrils. The attachment of three lysines to Aβ(10-35) gave the formation of remarkably long fibrils, while three glutamates resulted in a faster formation rate of the fibrils.

In this paper, we propose a strategy to predict the subcellular locations of proteins by combining various feature selection methods. Firstly, proteins are coded by amino-acid composition and physicochemical properties, then these features are arranged by Minimum Redundancy Maximum Relevance method and further filtered by feature selection procedure. Nearest Neighbor Algorithm is used as a prediction model to pre Read More

Band assignment for oxy, deoxy and methemoglobin using orbital promotion is crucial to understanding inter-relation of electronic transitions. Spectral changes may be correlated with conformational alterations. Conformational changes of hemoglobin were interpreted using four-orbital model of Gouterman. Our results indicated that Goutherman model can predict the predominant conformations of hemoglobin.

Lipoxygenases (LOXs, EC 1.13.11.12) are a class of non-heme iron containing dioxygenases which catalyze the regiospecific and stereospecific hydroperoxidation of polyunsaturated fatty acids with 1,4-pentadiene system such as linoleic acid and linolenic acid in plants. In this work we studied the LOX activity in damaged as well as in distal leaves in response to specialist (Agraulis vanillae vanillae) or generalist (Spodopte Read More

Rho GTPase controls multiple signal-transduction pathways involving the actin cytoskeleton and the microtubule cytoskeleton in processes such as the cell cycle, morphogenesis, and cell migration. The activity of Rho GTPases, such as Rac1, Cdc42, and RhoA, is regulated by GTPase-activating proteins (GAPs), guanine nucleotide exchange factors (GEFs), and guanine nucleotide dissociation inhibitor (GDI). The GEFs activate Rho Read More

Hop is a tetratricopeptide repeat domain (TPR)-containing co-chaperone that is able to directly associate with both Hsp70 and Hsp90. Previous data showed that the TPR2A-domain is the primary site for dimerization and that the TPR2B-domain may also play a role in dimerization. We present Hop-D456G, a mutant within the TPR2B-domain, that is a mixture of monomeric and dimeric species.

A new class of 1,4-substituted 1,2,3-triazole-based unnatural amino acids is demonstrated by employing click reaction between N-Fmoc amino alkyl azides and propiolic acid. The resulting unnatural amino acids were isolated and then subjected to Fmoc deprotection to isolate 1,2,3-triazole based amino acids as stable solids. These new class of molecules were also used for chain extension from both N- and C-terminals to synthesiz Read More

The Hierarchical Domain-Wise Alignment (HDWA) technique of domain identification in proteins is presented. HDWA is designed to identify hierarchically organized dynamic domains in proteins using the MD trajectories by eliminating systematic motions from MD trajectories recursively in a model-free manner. The method is tested on the proteins from different structural classes.

Granulysin is a human polypeptide produced by cytolytic cells active against a broad range of microbes. Three peptides covering the regions 25-50 (Gr-1 and Gr-2) and 39-62 (Gr-3) of granulysin were synthesized, and their in vitro activity against Mycobacterium tuberculosis was evaluated. The most active peptide was Gr-1C, containing a disulphide bridge, with Minimal Inhibitory Concentration value of 10.1 μM. In concentrations Read More

In this work, we isolated and characterized novel antifungal proteins from seeds of dandelion (Taraxacum officinale Wigg.). We showed that they are represented by five isoforms, each consisting of two disulphide-bonded large and small subunits. One of them, To-A1 was studied in detail, including N-terminal amino acid sequencing of both subunits, and shown to display sequence homology with the sunflower 2S albumin. Read More

The understanding of evolutionary mechanism is important, and equally important is to describe the evolutionary process. If so, we would know where the biological evolution will go. At species level, we would know whether and when a species will extinct or be prosperous. At protein level, we would know when a protein family will mutate more. In our previous study, we explored the possibility of using the differential equati Read More

A novel small antifungal peptide-producing strain D4 was isolated from the dung of wild plateau yak and identified as Bacillus megaterium. The purification procedure of peptide consisted of acid precipitation, methanol extract and C18 reverse-phase chromatography. The amino acid composition of peptide YP differed from those of antifungal peptides which have been reported to date. Peptide YP was proved to be a n Read More