Structural studies of protein unfolding

Methods for macromolecular structure determination (NMR and crystallography) are now being used to get structural information on partially folded and unfolded states of proteins. These techniques, in combination with proton hydrogen exchange studies are powerful tools to extract information on non-native states of proteins. This review discusses progress In this area of protein folding.

Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions

In this article, we present a novel application of a quantum clustering (QC) technique to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. We further portray each conformational population in terms of dynamically stable network parameters which beautifully capture the ligand induced variations in the ensemble in atomistic detail. The conformational populations thus identified by the QC method and verified by network parameters are evaluated for different ligand bound states of the protein pyrrolysyl-tRNA synthetase (DhPylRS) from D. hafniense. The ligand/environment induced re-distribution of protein conformational ensembles forms the basis for understanding several important biological phenomena such as allostery and enzyme catalysis. The atomistic level characterization of each population in the conformational ensemble in terms of the re-orchestrated networks of amino acids is a challenging problem, especially when the changes are minimal at the backbone level. Here we demonstrate that the QC method is sensitive to such subtle changes and is able to cluster MD snapshots which are similar at the side-chain interaction level. Although we have applied these methods on simulation trajectories of a modest time scale (20 ns each), we emphasize that our methodology provides a general approach towards an objective clustering of large-scale MD simulation data and may be applied to probe multistate equilibria at higher time scales, and to problems related to protein folding for any protein or protein-protein/RNA/DNA complex of interest with a known structure.

Water-mediated ionic interactions in protein structures

It is well known that water molecules play an indispensable role in the structure and function of biological macromolecules. The water-mediated ionic interactions between the charged residues provide stability and plasticity and in turn address the function of the protein structures. Thus, this study specifically addresses the number of possible water-mediated ionic interactions, their occurrence, distribution and nature found in 90% non-redundant protein chains. Further, it provides a statistical report of different charged residue pairs that are mediated by surface or buried water molecules to form the interactions. Also, it discusses its contributions in stabilizing various secondary structural elements of the protein. Thus, the present study shows the ubiquitous nature of the interactions that imparts plasticity and flexibility to a protein molecule.

Stochastic dynamics modeling of the protein sequence length distribution in genomes: implications for microbial evolution

In this paper, we report an analysis of the protein sequence length distribution for 13 bacteria, four archaea and one eukaryote whose genomes have been completely sequenced, The frequency distribution of protein sequence length for all the 18 organisms are remarkably similar, independent of genome size and can be described in terms of a lognormal probability distribution function. A simple stochastic model based on multiplicative processes has been proposed to explain the sequence length distribution. The stochastic model supports the random-origin hypothesis of protein sequences in genomes. Distributions of large proteins deviate from the overall lognormal behavior. Their cumulative distribution follows a power-law analogous to Pareto's law used to describe the income distribution of the wealthy. The protein sequence length distribution in genomes of organisms has important implications for microbial evolution and applications. (C) 1999 Elsevier Science B.V. All rights reserved.

Characterization of alkyl chain conformation in an intercalated cationic lipid bilayer by IR spectroscopy

A structural analysis of alkyl chain conformation of an intercalated cationic lipid bilayer is described. Dialkyl dimethylammonium ions (di-C(n)DA) were ion exchanged into the galleries of layered cadmium thiophosphate to give Cd0.83PS3(di-C(n)DA)(0.34). The grafting density and interlayer expansions were identical to those for the intercalated single chain alkyl trimethylammonium (C(n)TA) bilayers. The increased methylene chain density in the galleries, however, forces the intercalated lipid to adopt a more trans ordered structure. Progression bands arising from the coupling of vibrational modes of trans methylene units are used to establish the extent of trans registry. Two types of ordered structures of the intercalated cationic lipid may be distinguished. One in which both alkyl chains adopt an all-trans geometry, and one in which the methylene bond adjacent to the headgroup on one of the alkyl chains is gauche. The latter structure is typically found in the crystalline state of these cationic lipids. The concentrations of the two structures were determined from the ratio of the intensities of the progression bands and were found to remain unchanged with temperature.

iPBA: a tool for protein structure comparison using sequence alignment strategies

With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman-Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of similar to 88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA(+) in > 80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient `sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.

PRUNE and PROBE-two modular web services for protein-protein docking

The protein-protein docking programs typically perform four major tasks: (i) generation of docking poses, (ii) selecting a subset of poses, (iii) their structural refinement and (iv) scoring, ranking for the final assessment of the true quaternary structure. Although the tasks can be integrated or performed in a serial order, they are by nature modular, allowing an opportunity to substitute one algorithm with another. We have implemented two modular web services, (i) PRUNE: to select a subset of docking poses generated during sampling search (http://pallab.serc.iisc.ernet.in/prune) and (ii) PROBE: to refine, score and rank them (http://pallab.serc.iisc.ernet.in/probe). The former uses a new interface area based edge-scoring function to eliminate > 95% of the poses generated during docking search. In contrast to other multi-parameter-based screening functions, this single parameter based elimination reduces the computational time significantly, in addition to increasing the chances of selecting native-like models in the top rank list. The PROBE server performs ranking of pruned poses, after structure refinement and scoring using a regression model for geometric compatibility, and normalized interaction energy. While web-service similar to PROBE is infrequent, no web-service akin to PRUNE has been described before. Both the servers are publicly accessible and free for use.

Helical structures: The geometry of protein helices and nanotubes

In nature, helical structures arise when identical structural subunits combine sequentially, the orientational and translational relation between each unit and its predecessor remaining constant. A helical structure is thus generated by the repeated action of a screw transformation acting on a subunit. A plane hexagonal lattice wrapped round a cylinder provides a useful starting point for describing the helical conformations of protein molecules, for investigating the geometrical properties of carbon nanotubes, and for certain types of dense packings of equal spheres.

Mapping of B-cell epitopes of hemagglutinin protein of rinderpest virus

Monoclonal antibodies (mAbs) against secreted hemagglutinin (H) protein of rinderpest virus (RPV) expressed by a recombinant baculovirus were generated to characterize the antigenic sites on H protein and regions of functional significance. Three of the mAbs displayed hemagglutination inhibition activity and these mAbs were unable to neutralize virus infectivity. Western immunoblot analysis of overlapping deletion mutants indicated that three mAbs recognize antigenic regions at the extreme carboxy terminus (between amino acids 569 and 609) and the fourth mAb between amino acids 512 and 568. Using synthetic peptides, aa 569-577 and 575-583 were identified as the epitopes for E2G4 and D2F4, respectively. The epitopic domains of A12A9 and E2B6 mAbs were mapped to regions encompassing aa 527-554 and 588-609. Two epitopes spanning the extreme carboxy terminal region of aa 573 to 587 and 588 to 609 were shown to be immunodominant employing a competitive ELISA with polyclonal sera form vaccinated cattle. The D2F4 mAb which recognizes a unique epitope on RPV-H is not present on the closely related peste des petits ruminant virus FIN protein and this mAb could serve as a tool in the seromonitoring program after rinderpest vaccination. (C) 2002 Elsevier Science (USA).

Novel cationic and neutral analogues of bile acids: Synthesis and preliminary study of their aggregation properties

Novel cationic and neutral analogues of bile acids (1-6) were synthesized and their aggregation properties studied. Cations 1 and 2 formed thermoreversible gels in aqueous salt solutions, whereas neutral 4 formed gels in water in the presence of organic solvents such as ethanol, methanol, DMSO, and DMF. The gels derived from 1 and 4 have been investigated by SEM and with pyrene as a fluorescent probe.

PDB Goodies - a web-based GUI to manipulate the Protein Data Bank file

PDB Goodies is a web-based graphical user interface (GUI) to manipulate the Protein Data Bank file containing the three-dimensional atomic coordinates of protein structures. The program also allows users to save the manipulated three-dimensional atomic coordinate file on their local client system. These fragments are used in various stages of structure elucidation and analysis. This software is incorporated with all the three-dimensional protein structures available in the Protein Data Bank, which presently holds approximately 18 000 structures. In addition, this program works on a three-dimensional atomic coordinate file (Protein Data Bank format) uploaded from the client machine. The program is written using CGI/PERL scripts and is platform independent. The program PDB Goodies can be accessed over the World Wide Web at http:// 144.16.71.11/pdbgoodies/.

Synthesis of acicular hydrogoethite (alpha-FeOOH center dot xH(2)O; 0.1 < x < 0.22) particles using morphology controlling cationic additives and magnetic properties of maghemite derived from hydrogoethite

A method for the preparation of acicular hydrogoethite (alpha -FeOOH.xH(2)O, 0.1 < x < 0.22) particles of 0.3-1 mm length has been optimized by air oxidation of Fe( II) hydroxide gel precipitated from aqueous (NH4)(2)Fe(SO4)(2) solutions containing 0.005-0.02 atom% of cationic Pt, Pd or Rh additives as morphology controlling agents. Hydrogoethite particles are evolved from the amorphous ferrous hydroxide gel by heterogeneous nucleation and growth. Preferential adsorption of additives on certain crystallographic planes thereby retarding the growth in the perpendicular direction, allows the particles to acquire acicular shapes with high aspect ratios of 8-15. Synthetic hydrogoethite showed a mass loss of about 14% at similar to 280 degreesC, revealing the presence of strongly coordinated water of hydration in the interior of the goethite crystallites. As evident from IR spectra, excess H2O molecules (0.1- 0.22 per formula unit) are located in the strands of channels formed in between the double ribbons of FeO6 octahedra running parallel to the c- axis. Hydrogoethite particles constituted of multicrystallites are formed with Pt as additive, whereas single crystallite particles are obtained with Pd (or Rh). For both dehydroxylation as well as H-2 reduction, a lower reaction temperature (similar to 220 degreesC) was observed for the former (Pt treated) compared to the latter (Pd or Rh) (similar to 260 degreesC). Acicular magnetite (Fe3O4) was prepared either by reducing hydrogoethite (magnetite route) or dehydroxylating hydrogoethite to hematite and then reducing it to magnetite (hematite- magnetite route). According to TEM studies, preferential dehydroxylation of hydrogoethite along < 010 > leads to microporous hematite. Maghemite (gamma -Fe2O3 (-) (delta), 0 < < 0.25) was obtained by reoxidation of magnetite. The micropores are retained during the topotactic transformation to magnetite and finally to maghemite, whereas cylindrical mesopores are formed due to rearrangement of the oxygen sublattice from hexagonal to cubic close packing during the conversion of hydrogoethite to magnetite and then to maghemite. Accordingly, three different types of maghemite particles are realized: strongly oriented multicrystalline particles, single crystalline acicular particles with micropores or crystallites having mesopores. Higher values of saturation magnetization ((s) = 74 emu g(-1)) and coercivity (H-c = 320 Oe) are obtained for single crystalline mesoporous particles. In the other cases, the smaller size of particles and larger distribution of micropores decreases sigma (s) considerably ( < 60 emu g(-1)) due to relaxation effects of spins on the surface atoms as revealed by Mossbauer spectroscopy.

Synthesis of novel cationic lipids with fully or partially non-scissile linkages between the hydrocarbon chains and pseudoglyceryl backbone

Five novel cationic lipids with fully or partially non-scissile linkage regions between the pseudoglyceryl backbone and the hydrocarbon chains have been synthesized. The membrane-forming properties of these new lipids are briefly presented.