The Design and Construction of Synthetic Protein Mimics

A strategy for the modular construction of synthetic protein mimics based on the ability non-protein amino acids to act as stereochemical directors of polypeptide chain folding, is described. The use of alpha-aminoisobutyric acid (Aib) to construct stereochemically rigid helices has been exemplified by crystallographic and spectroscopic studies of several apolar peptides, ranging in length from seven to sixteen residues. The problem of linker design in elaborating alpha,alpha motifs has been considered. Analysis of protein crystal structure data provides a guide to choosing linking sequences. Attempts at constructing linked helical motifs using linking Gly-Pro segments have been described. The use of flexible linkers, like epsilon-aminocaproic acid has been examined and the crystallographic and solution state analysis of a linked helix motif has been presented. The use of bulky sidechain modifications on a helical scaffold, as a means of generating putative binding sites has been exemplified by a crystal structure of a peptide packed in a parallel zipper arrangement.

INDUCTION OF FOLDED STRUCTURES IN DESIGNED PEPTIDES USING CONFORMATIONALLY CONSTRAINED RESIDUES

Folding into compact globular structures, with well-defined modules of secondary structure, appears to be a characteristic of long polypeptide chains, with a specific patterning of coded amino acid residues along the length of sequence. Cooperative hydrogen bond driven secondary structure formation and solvent forces, which contribute favorably to the entropy of folding, by promoting compaction of the polymeric chain, have long been discussed as major determinants of the folding process. First principles design approaches, which use non-coded amino acids, employ an alternative structure directing strategy, by using amino acid residues which exhibit a strong conformational bias for specific regions of the Ramachandran map. This overview of ongoing studies in the authors' laboratory, attempts to explore the use of conformationally restricted amino acid residues in the design of peptides with well-defined secondary structures. Short peptides composed of 20 genetically coded amino acids usually exist in solution as an ensemble of equilibrating conformations. Apolar peptide sequences, which are readily soluble in organic solvents like chloroform and methanol, facilitate formation of structures which are predominately driven by intramolecular hydrogen bond formation. The choice of sequences containing residues with a limited range of conformational choices strongly favors formation of local turn structures, stabilized by short range intramolecular hydrogen bonds. Two residue beta-turns can nucleate either helical or hairpin folding, depending on the precise conformation of the turn segment Restriction of the conformational space available to amino acid residues is easily achieved by introduction of an additional alkyl group at the C alpha carbon atom or by side chain backbone cyclization, as in proline. Studies of synthetic sequences incorporating two prototype residues alpha-aminoisobutyric acid (Aib) and D-proline (DPro) illustrate the utility of the strategy in construction of helices and hairpins. Extensions to the design of conformationally switchable sequences and structurally defined hybrid peptides containing backbone homologated residues are also surveyed.

Conformation-activity correlations for chemotactic tripeptide analogs incorporating dialkyl residues with linear and cyclic alkyl sidechains at position 2

Five stereochemically constrained analogs of the chemotactic tripeptide incorporating 1-aminocycloalkane-1-carboxylic acid (Ac(n)c) and alpha,alpha-dialkylglycines (Deg, diethylglycine; Dpg, n,n-dipropylglycine and Dbg, n,n-dibutylglycine) at position 2 have been synthesized. NMR studies of peptides For-Met-Xxx-Phe-OMe (Xxx = Ac(7)c, I; Ac(8)c, II; Deg, III; Dpg, IV and Dbg, V; For, formyl) establish that peptides with cycloalkyl residues, I and II, adopt folded beta-turn conformations in CDCl3 and (CD3)(2)SO. In contrast, analogs with linear alkyl sidechains, III-V, favour fully extended (C-5) conformations in solution. Peptides I-V exhibit high activity in inducing beta-glucosaminidase release from rabbit neutrophils, with ED(50) values ranging from 1.4-8.0 x 10(-11)M. In human neutrophils the Dxg peptides III-V have ED(50) values ranging from 2.3 x 10(-8) to 5.9 x 10(-10) M, with the activity order being V > IV > III. While peptides I-IV are less active than the parent. For-Met-Leu-Phe-OH, in stimulating histamine release from human basophils, the Dbg peptide V is appreciably more potent, suggesting its potential utility as a probe for formyl peptide receptors.

Steam-cured stabilised soil blocks for masonry construction

Energy-efficient, economical and durable building materials are essential for sustainable construction practices. The paper deals with production and properties of energy-efficient steam-cured stabilised soil blocks used fbr masonry construction. Problems of mixing expansive soil and lime, and production of blocks using soil-lime mixtures have been discussed briefly. Details of steam curing of stabilised soil blocks and properties of such blocks are given. A comparison of energy content of steam-cured soil blocks and burnt bricks is presented. It has been shown that energy-efficient steam cured soil blocks (consuming 35% less thermal energy compared to burnt clay bricks) having high compressive strength can be easily produced in a decentralised manner.

Efficient Output-Sensitive Construction of Reeb Graphs

The Reeb graph tracks topology changes in level sets of a scalar function and finds applications in scientific visualization and geometric modeling. This paper describes a near-optimal two-step algorithm that constructs the Reeb graph of a Morse function defined over manifolds in any dimension. The algorithm first identifies the critical points of the input manifold, and then connects these critical points in the second step to obtain the Reeb graph. A simplification mechanism based on topological persistence aids in the removal of noise and unimportant features. A radial layout scheme results in a feature-directed drawing of the Reeb graph. Experimental results demonstrate the efficiency of the Reeb graph construction in practice and its applications.

Biomethanation of herbaceous biomass residues using 3-zone plug flow like digesters - A case study from India

Biomethanation of herbaceous biomass feedstock has the potential to provide clean energy source for cooking and other activities in areas where such biomass availability predominates. A biomethanation concept that involves fermentation of biomass residues in three steps, occurring in three zones of the fermentor is described. This approach while attempting take advantage of multistage reactors simplifies the reactor operation and obviates the need for a high degree of process control or complex reactor design. Typical herbaceous biomass decompose with a rapid VFA flux initially (with a tendency to float) followed by a slower decomposition showing balanced process of VFA generation and its utilization by methanogens that colonize biomass slowly. The tendency to float at the initial stages is suppressed by allowing previous days feed to hold it below digester liquid which permits VFA to disperse into the digester liquid without causing process inhibition. This approach has been used to build and operate simple biomass digesters to provide cooking gas in rural areas with weed and agro-residues. With appropriate modifications, the same concept has been used for digesting municipal solid wastes in small towns where large fermentors are not viable. With further modifications this concept has been used for solid-liquid feed fermentors. Methanogen colonized leaf biomass has been used as biofilm support to treat coffee processing wastewater as well as crop litter alternately in a year. During summer it functions as a biomass based biogas plants operating in the three-zone mode while in winter, feeding biomass is suspended and high strength coffee processing wastewater is let into the fermentor achieving over 90% BOD reduction. The early field experience of these fermentors is presented.

Chemical Modification Studies of Gelonin - Involvement of Arginine Residues in Biological-Activity

Gelonin inhibits protein synthesis by inactivating the eukaryotic 60 S ribosomal subunit by an unknown mechanism. The protein was purified in high yield by a new method using Cibacron blue F3GA-Sepharose. Chemical modification studies reveal that arginine residues are essential for biological activity.

Interaction Between Two Residues in the Inter-Domain Interface of Escherichia coli Peptidase N Modulates Catalytic Activity

The role of interaction between Asn259 (catalytic domain) with Gln821 (C-terminal domain) in PeptidaseN was investigated. The k(cat) of PeptidaseN containing Asn259Asp or Gln821Glu is enhanced whereas it is suppressed in Asn259AspGln821Glu. Structural analysis shows this interaction to change the relative disposition of active site residues, which modulates catalytic activity.

Electroleaching of Zinc leach residues

A room-temperature cathodic electrolytic process was developed in the laboratory to recover zinc from industrial leach residues. The various parameters affecting the electroleaching process were studied using a statistically designed experiment. To understand the mechanisms behind the electrode processes, cyclic voltammetry and galvanostatic studies were carried out. The role of Einh measurements in monitoring such an electroleaching procedure is also shown. Since significant amounts of iron were also present in the leach liquor, attempts were made to purify it before zinc recovery by electrowinning. Reductive dissolution and creation of anion vacancies were found to be responsible for the dissolution of zinc ferrite present in the leach residue. A flow sheet of the process is given.

Systematic Construction of Linear Transform Based Full-Diversity, Rate-One Space-Time Frequency Codes

In this paper, we generalize the existing rate-one space frequency (SF) and space-time frequency (STF) code constructions. The objective of this exercise is to provide a systematic design of full-diversity STF codes with high coding gain. Under this generalization, STF codes are formulated as linear transformations of data. Conditions on these linear transforms are then derived so that the resulting STF codes achieve full diversity and high coding gain with a moderate decoding complexity. Many of these conditions involve channel parameters like delay profile (DP) and temporal correlation. When these quantities are not available at the transmitter, design of codes that exploit full diversity on channels with arbitrary DIP and temporal correlation is considered. Complete characterization of a class of such robust codes is provided and their bit error rate (BER) performance is evaluated. On the other hand, when channel DIP and temporal correlation are available at the transmitter, linear transforms are optimized to maximize the coding gain of full-diversity STF codes. BER performance of such optimized codes is shown to be better than those of existing codes.

Synthetic studies towards the phloroglucin natural product hyperforin: construction of the fully prenylated bicyclic core

An approach towards the highly functionalized bicyclo[3.3.1]nonan-9-one core of the complex PPAP-based natural product hyperforin, with the full complement of prenyl substituents in required stereo-disposition, is delineated.

Studies on tryptophan residues of Abrus agglutinin Stopped-flow kinetics of modification and fluorescence-quenching studies

The presence of two essential tryptophan residues/molecule was implicated in the binding site of Abrus agglutinin [Patanjali, Swamy, Anantharam, Khan & Surolia (1984) Biochem. J. 217, 773-781]. A detailed study of the stopped-flow kinetics of the oxidation of tryptophan residues revealed three classes of tryptophan residues in the native protein. A discrete reorganization of tryptophan residues into two phases was observed upon ligand binding. The heterogeneity of tryptophan exposure was substantiated by quenching studies with acrylamide, succinimide and Cs+. Our study revealed the microenvironment of tryptophan residues to be hydrophobic, and also the presence of acidic amino acid residues in the vicinity of surface-localized tryptophan residues.

An (O)over-tilde(mn) Gomory-Hu Tree Construction Algorithm for Unweighted Graphs

We present a fast algorithm for computing a Gomory-Hu tree or cut tree for an unweighted undirected graph G = (V, E). The expected running time of our algorithm is (O) over tilde (mc) where vertical bar E vertical bar = m and c is the maximum u-v edge connectivity, where u, v is an element of V. When the input graph is also simple (i.e., it has no parallel edges), then the u-v edge connectivity for each pair of vertices u and v is at most n - 1; so the expected run-ning time of our algorithm for simple unweighted graphs is (O) over tilde (mn). All the algorithms currently known for constructing a Gomory-Hu tree [8, 9] use n - 1 minimum s-t cut (i.e., max flow) subroutines. This in conjunction with the current fastest (O) over tilde (n(20/9)) max flow algorithm due to Karger and Levine[11] yields the current best running time of (O) over tilde (n(20/9)n) for Gomory-Hu tree construction on simple unweighted graphs with m edges and n vertices. Thus we present the first (O) over tilde (mn) algorithm for constructing a Gomory-Hu tree for simple unweighted graphs. We do not use a max flow subroutine here; we present an efficient tree packing algorithm for computing Steiner edge connectivity and use this algorithm as our main subroutine. The advantage in using a tree packing algorithm for constructing a Gomory-Hu tree is that the work done in computing a minimum Steiner cut for a Steiner set S subset of V can be reused for computing a minimum Steiner cut for certain Steiner sets S' subset of S.

Convenient construction of tetrahedral finite elements for the quasi-harmonic equation

It is shown that in the finite-element formulation of the general quasi-harmonic equation using tetrahedral elements, for every member of the element family there exists just one numerical universal matrix indpendent of the size, shape and material properties of the element. Thus the element matrix is conveniently constructed by manipulating this single matrix along with a set of reverse sequence codes at the same time accounting for the size, shape and material properties in a simple manner.