Mirrors in the PDB: left-handed α-turns guide design with D-amino acids

<p>Abstract</p> <p>Background</p> <p>Incorporating variable amino acid stereochemistry in molecular design has the potential to improve existing protein stability and create new topologies inaccessible to homochiral molecules. The Protein Data Bank has been a reliable, rich source of information on molecular interactions and their role in protein stability and structure. D-amino acids rarely occur naturally, making it difficult to infer general rules for how they would be tolerated in proteins through an analysis of existing protein structures. However, protein elements containing short left-handed turns and helices turn out to contain useful information. Molecular mechanisms used in proteins to stabilize left-handed elements by L-amino acids are structurally enantiomeric to potential synthetic strategies for stabilizing right-handed elements with D-amino acids.</p> <p>Results</p> <p>Propensities for amino acids to occur in contiguous α_Lhelices correlate with published thermodynamic scales for incorporation of D-amino acids into α_Rhelices. Two backbone rules for terminating a left-handed helix are found: an α_Rconformation is disfavored at the amino terminus, and a β_Rconformation is disfavored at the carboxy terminus. Helix capping sidechain-backbone interactions are found which are unique to α_Lhelices including an elevated propensity for L-Asn, and L-Thr at the amino terminus and L-Gln, L-Thr and L-Ser at the carboxy terminus.</p> <p>Conclusion</p> <p>By examining left-handed α-turns containing <smcaps>L</smcaps>-amino acids, new interaction motifs for incorporating <smcaps>D</smcaps>-amino acids into right-handed α-helices are identified. These will provide a basis for <it>de novo </it>design of novel heterochiral protein folds.</p

Studies on crossability in cashew (Anacardium occidentale L.) genotypes

Successful hybridization primarily depends on the crossability of the parents involved as well as development of the F1 hybrids and their derivatives. In the present study, 12 crosses were attempted to study the crossability relationship among cashew genotypes. Among the crosses, the highest crossability was recorded in the cross H-303 x VTH 711/4 (17.16%), whereas, high rate of abscission of young fruits was observed in crosses involving NRCC Selection -2 as female parent. The genotype VTH 711/4 has shown substantially high per cent of crossability and better nut set with different genotypes of cashew

Novel food packaging technologies: Innovations and future prospective

AbstractNovel food packaging technologies arose as a result of consumer’s desire for convenient, ready to eat, tasty and mild processed food products with extended shelf life and maintained quality. Recent trend of lifestyle changes with less time for consumers to prepare foods posed a great challenge toward food packaging sector for the evolution of novel and innovative food packaging techniques. The novel food packaging techniques, viz. active packaging, intelligent packaging and bio active packaging which involve intentional interaction with the food or its surroundings and influence on consumer’s health have been the major innovations in the field of packaging technology. These novel techniques act by prolonging the shelf life, enhancing or maintaining the quality, providing indication and to regulate freshness of food product. The advancement in novel food packaging technologies involves retardation in oxidation, hindered respiratory process, prevention of microbial attack, prevention of moisture infusion, use of CO2 scavengers/emitters, ethylene scavengers, aroma emitters, time-temperature sensors, ripeness indicators, biosensors and sustained release of antioxidants during storage. The novel food packaging technologies besides the basic function of containment increase the margin of food quality and safety. The novel food packaging techniques thus help in fulfilling the demands throughout the food supply chain by gearing up toward persons own lifestyle. The main objectives of this review article are to provide basic knowledge of different new and innovative food packaging techniques about their way of preservative action, effectiveness and suitability in various types of foods

English Teaching to Engineering Students difficulties and Solutions

Being science student and wondering about robots, electrons, engineering students hardly bother about nouns, verbs and tenses. English no doubt has taken place as first language in the corporate world but heart of an engineering student still resist the panorama of English language in their lives. Subconsciously aware of the importance of communication skills in getting a job, they fail to realize its importance consciously in the class rooms. They fail to realize that the gateway to express their core knowledge is communication skill only. Maximum engineering students neglect this most important skill because of many reasons. Though there might be many argumentations which favor causing lack of interest in English learning process but its importance cannot be neglected. This research basically focus on the reasons ;why engineering /business students lack interest in learning of communication skills and what tentative pedagogies can be adopted to develop their interest in learning of communication skills. This research paper aims to find out the difficulties in teaching, learning of English/communication skills to engineering students and tentative solutions to ease the process of learning. Keywords: communication skills, practical learning, listening skill, improve expression, communication skills in present scenario, Non verbal communicatio

Dynamic Surface Charts for Scattered 4-D Data in Excel Spreadsheets

Visualizations that are low-cost in memory are desirable. We present a method for stitching three-dimensional scattered data from multiple worksheets into a dynamic “animation-like” surface chart in Excel. This method is useful when (1) the user hard-codes the data points to conserve memory; employing such strategy scales better than soft-coding data values, (2) the data values are hard-coded by an unknown source, or (3) the function is complex and requires a user-defined function to output values into cells. In particular, we demonstrate an application in biology where rigid motion (rotation and translation are the only transformations applied to an object in 3-D space) is used to model the free energy gain/loss by surveying various placements and orientations of membrane proteins with respect to their environment. Our strategy involves a simple concept of scrolling through an order of worksheets, and can be extended to even more dimensions (i.e. scrolling through workbooks if necessary

Molecular Self-Assembly Strategy for Generating Catalytic Hybrid Polypeptides

Recently, catalytic peptides were introduced that mimicked protease activities and showed promising selectivity of products even in organic solvents where protease cannot perform well. However, their catalytic efficiency was extremely low compared to natural enzyme counterparts presumably due to the lack of stable tertiary fold. We hypothesized that assembling these peptides along with simple hydrophobic pockets, mimicking enzyme active sites, could enhance the catalytic activity. Here we fused the sequence of catalytic peptide CP4, capable of protease and esterase-like activities, into a short amyloidogenic peptide fragment of Aβ. When the fused CP4-Aβ construct assembled into antiparallel β- sheets and amyloid fibrils, a 4.0-fold increase in the hydrolysis rate of p-nitrophenyl acetate (p-NPA) compared to neat CP4 peptide was observed. The enhanced catalytic activity of CP4-Aβ assembly could be explained both by pre-organization of a catalytically competent Ser-His-acid triad and hydrophobic stabilization of a bound substrate between the triad and p-NPA, indicating that a design strategy for self-assembled peptides is important to accomplish the desired functionality

Using α-Helical Coiled-Coils to Design Nanostructured Metalloporphyrin Arrays

We have developed a computational design strategy based on the alpha-helical coiled-coil to generate modular peptide motifs capable of assembling into metalloporphyrin arrays of varying lengths. The current study highlights the extension of a two-metalloporphyrin array to a four-metalloporphyrin array through the incorporation of a coiled-coil repeat unit. Molecular dynamics simulations demonstrate that the initial design evolves rapidly to a stable structure with a small rmsd compared to the original model. Biophysical characterization reveals elongated proteins of the desired length, correct cofactor stoichiometry, and cofactor specificity. The successful extension of the two-porphyrin array demonstrates how this methodology serves as a foundation to create linear assemblies of organized electrically and optically responsive cofactors

Energetic Selection of Topology in Ferredoxins

Models of early protein evolution posit the existence of short peptides that bound metals and ions and served as transporters, membranes or catalysts. The Cys-X-X-Cys-X-X-Cys heptapeptide located within bacterial ferredoxins, enclosing an Fe4S4 metal center, is an attractive candidate for such an early peptide. Ferredoxins are ancient proteins and the simple α+β fold is found alone or as a domain in larger proteins throughout all three kingdoms of life. Previous analyses of the heptapeptide conformation in experimentally determined ferredoxin structures revealed a pervasive right-handed topology, despite the fact that the Fe4S4 cluster is achiral. Conformational enumeration of a model CGGCGGC heptapeptide bound to a cubane iron-sulfur cluster indicates both left-handed and right-handed folds could exist and have comparable stabilities. However, only the natural ferredoxin topology provides a significant network of backbone-to-cluster hydrogen bonds that would stabilize the metal-peptide complex. The optimal peptide configuration (alternating αL,αR) is that of an α-sheet, providing an additional mechanism where oligomerization could stabilize the peptide and facilitate iron-sulfur cluster binding