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Report is presented on the binary complex structures of enzyme PrnB with D and L-tryptophan and D and L-7-chloro-tryptophan. The structures identify a common hydrophobic pocket for the indole ring but exhibit unusual heme ligation and substrate binding when compared with the tryptophan 2,3-dioxygenase crystal structures.

S100B is a calcium-binding protein, which binds calcium and also undergoes certain changes, exposing the hydrophobic surface residues. Such conformational changes help the protein to interact with various biological target molecules, also maintaining a balance between the amide exchange rates.

The study explains the phenomenon of protein nitration, which is found to play a very critical role in the onset and progression of several neurodegenerative diseases. The analysis shows that nitration modifies protein function by altering the hydrophobicity, hydrogen bonding and electrostatic properties of the targeted protein.

The effects of the turn, the hydrophobic cluster, and a disulfide cross-linker on the folding kinetics of a designed alpha-helical hairpin, Z34C, are examined using an infrared temperature-jump method in conjunction with site-specific mutagenesis. Results reveal that Z34C folds with an ultrafast rate and support a folding mechanism in which the rate-limiting step corresponds to the formation of the reverse turn.

Thermophile Hydrogenobacter thermophilus cytochrome c552 (HT) is a stable protein, which has a denaturation temperature [T.sub.m)) of 109.8 and 129.7 degree Celsius for the oxidized and reduced forms, respectively. The removal of a single hydroxyl group from the hydrophobic core of HT, through the replacement of a Tyr by Phe, was found to result in further elevation of the [T.sub. m) value of the oxidized form by approximately 6 degree Celsius, the [T.sub. m) value of the reduced one remaining essentially unaltered.

The contribution of hydrophobic interactions to the dimerization of the prolyl dipepetidase DPP-IV was investigated. Results revealed that hydrophobic residues F713, W734 and Y735 were essential for DPP-IV dimerization and the enzymatic activity of DPP-IV was correlated with its quaternary structure.

Study is conducted to show that the hydrophobic loop is mobile in F- as well as in G-action, fluctuating between the extended and parked conformations. The results show that loop 262-274 fluctuations in G- and F- actin and correlate loop dynamics with actin filament formation and stability.

Evidence that signal sequences that are poor integration effectors can promote integration under experimental conditions that allow nascent chain more time to integrate is presented. Through the analysis of the prolactin signal sequence it is found that the N terminal and hydrophobic regions of the signal sequence affect integration most significantly.

Model membrane-inserted Lys-flanked polyLeu peptides (pL peptides) containing one or two Asp substitutions at different positions in their primary sequence are studied with reference to their behavior. At low pH (where the Asp residues were uncharged), the fully transmembrane (TM) state in which the Asp residues were buried in the bilayer core predominated while at higher pH (where the Asp residues were charged), the formation of a truncated TM helix or a shallowly located non-TM state was observed.

Studies done to examine the ability of free fatty acids (FFA) to activate phospholipase C delta1(PLC delta1) are reported. Results of the study demonstrate that esterified and nonesterified fatty acids can bind to and regulate protein function, identifying a functional role for hydrophobic interactions between lipids and proteins.

Combinatorial biosynthetic procedures in the producing organisms is used to examine the binding Characteristics of m ithramycin and c hromomycin a nalogues to the minor groove of G/C-rich regions in DNA in the presence of dications such as [Mg.sub.2] and discover new pathways to structurally related molecules exhibiting both lower toxicity and higher biological activity. Entropically driven DNA binding which is dominated by the hydrophobic transfer of every compound from solution into the minor groove of DNA revealed the analogues, mithramycin SDK and chromomycin SDK to possess the higher DNA binding affinities.

A study is conducted to characterize kinetic and thermodynamic phases in the preconformational folding process of bovine pancreatic ribonuclease A coupled with fast SS formation and SS reshuffling. The transition from kinetic to thermodynamic phase which stabilized SS intermediates is observed to be induced by hydrophobic nucleation as well as generation of the native interactions.

Solid-state nuclear magnetic resonance spectroscopy is used to determine the conformation, dynamics, oligomeric state and topology of a human [alpha]-defensin, HNP-1, in DMPC/DMPG bilayers. The presence of a small fraction of monomers and the shallower insertion at lower protein concentrations provide insight into the concentration-dependent oligomerization and membrane-bound structure adopted by the HNP-1 and mechanism of action of human [alpha]-defensins.

The crystal structures of the C-terminal peptide-binding domain of human Hsp40 Hdj1 (CTD) and of its complex with the C-terminal octapeptide of human Hsp70 are determined. The octapeptides are located in two sites and the roles of the two peptide-binding sites of Hdj1 are discussed.

The first X-ray crystal structures of DADH and its complexes with iminoarginine ([DADH.sub.red]/iminoarginine) and iminohistidine ([DADH.sub.red]/iminohistidine) are described. Comparison of the kinetic data for the activity of DADH on different D-amino acids and the crystal structures in complex with iminoarginine and iminohistidine has shown that the enzyme is analyzed by substrate specificity, being able to oxidize positively charged and large hydrophobic D-amino acids bound within a flask-like cavity.

Novel analogues of melittin were designed by substituting the leucine residue(s) at the 'd' and 'a' positions of its previously identified leucine zipper motif to understand the lytic activities of melittin antimicrobial peptide against bacteria and mammalian cells. The data revealed that the substitution of hydrophobic leucine residue(s) by lesser hydrophobic alanine residue(s) in the leucine zipper sequence of melittin disturbed its pore-forming activity and mechanism only in hRBCs but not in the tested bacteria.

The structural determinants of the folding kinetics of a naturally occurring helical hairpin (porcine PYY) that is free of disulfide bonds and metal ion-induced cross-links are studied by using an infrared temperature-jump technique. The results are interpreted in terms of a folding mechanism in which the turn is formed in the transition state and is also based on the assumption that cross-strand hydrophobic contacts are present in the thermally unfolded state of PYY.

Peptide-based and in vivo approaches are used for examining the role of the transmembrane (TM) domain in the formation of proteolipid protein (PLP) quaternary structure through homo-oligomeric helix-helix interactions. The results have shown that TM segments in misfolded PLP monomers that expose and create surface-exposed helix-helix interaction sites that are masked might have consequences for disease.

The structural and functional effects of alanine-to-serine substitutions in bilayer-spanning gramicidin channels are examined in order to analyze the consequences of burying polar, hydrogen-bonding hydroxyl groups within the hydrocarbon core of lipid bilayer membranes. The studies have shown that when compared to the corresponding Ala-containing reference channels, the polar Ser residues have decreased the analoguesE channel-forming potency, indicating a substantial energetic penalty for burying the polar Ser side chain in the bilayer hydrophobic core.

Chemical probes were applied to demonstrate that the surface hydrophobicities of cataract-associated Pro23 to Thr (P23T) mutants in human [gamma]D-crystallin (HGD) are inversely related to their solubility. The results provide direct evidence for the important role played by net hydrophobic and anisotropic protein-protein interactions in the aggregation of P23T.

Atomic force microscopy (AFM) under fluid was utilized to examine the interaction of the endophilin N-BAR domain with planar supported lipid bilayers, under conditions that closely mimic the environment in which this protein normally operates. The results for the action of the endophilin N-BAR domain under near-physiological conditions provide additional insight into its membrane binding and bending mechanism.

The feasibility of using solution phase [super 19]F nuclear magnetic resonance (NMR) was examined to study peptide-membrane interactions by utilizing the antimicrobial peptide MSI-78 as a model system. The result was in agreement with the structural models of MSI-78 bound to lipids and point to the feasibility of using fluorine-labeled peptides to monitor peptide-membrane interactions in living cells.

Well-characterized elastin-like polypeptides (ELP) containing three hydrophobic domains flanking two cross-linking domains is used to describe the effects of temperature, polypeptide concentration, and solution conditions on the kinetics of self-assembly of an elastin-like polypeptide tropoelastin. The results provide insight into the possible mechanisms for the spontaneous organization of such ELPs into extended networks.

The semisynthesis of a bacterial nonselective cation channel, NaK polypeptide that is assembled from a recombinantly expressed thioester peptide and a chemically synthesized peptide using the native chemical ligation reaction is reported. Functional characterization of the folded semisynthetic NaK channels indicates that it is functionally similar to the wild-type protein and the presence of a negatively charged residue in the vicinity of the ion binding sites is necessary for optimal flux of ions through the NaK channel.

The triple-helical structure of specific assembly signals designed within collagen peptides as a subunit in the higher-order assembly of unique biomaterials is described. The obtained nano- and microscale fibers, gels, spheres, and meshes could find potential use for novel biological applications in drug delivery, tissue engineering, and regenerative medicine.

The molecular features and binding properties of the green alga Scherffelia dubia centrin (SdCen), a member of the Chlamydomonas reinhardtii centrin (CrCen) subfamily are reported. The data obtained provide insight into the molecular mechanisms used by SdCen and probably by other algal centrins to respond to cellular [Ca.sup.2+] signals.

A study was conducted to distinguish between specific and nonspecific interactions of period 2 (PER2), an integral component in the negative feedback loop that establishes circadian rhythms in mammals which is identified as a heme-binding protein. The results indicated that heme binding to PER2 is likely to be nonspecific and does not involve the hydrophobic pocket within the PER2 PAS domains that in other PAS proteins commonly recognizes cofactors.

Deletion mutation technique was applied to study the role of the C-terminal loop L137-S141 in the folding and folding stability of staphylococcal nuclease (SNase). The results revealed that the stabilizing folding of the SNase and SNase fragments was largely influenced by the hydrophobic packing interactions in both the C-terminal local structural region surrounding W140 including the loop L137-S141 and the N-terminal local structural region of the '[beta]-barrel' hydrophobic core.

The use of 4-substituted proline derivatives to replace Pro62 and the effect of pucker conformation on the proline-aromatic interaction and the stability of HP36 are reported. The replacement of Pro62 to proline derivatives not only influenced the stereoelectronic effects induced by aromatic-proline interaction but also the steric and hydrophobic effects induced by the substituents which play an important role in modulating the stability of HP36.

The interfacial properties of both peptides were examined at the triolein/water interface to understand the interaction of apolipoprotein B (B6.4-13 and B13-17) with triacylglycerol during lipoprotein assembly. The results suggested that the N-terminal apoB starts recruiting lipid as early as B6.4 during lipoprotein assembly but additional sequences are essential for formation of a lipid pocket that could stabilize lipoprotein emulsion particles for secretion.

A 'remote' structurally conserved cluster of hydrophobic residues in the OMPDC from Methanobacter thermoautotrophicus that includes Val 182 in the active site loop assembled in the closed, catalytically active conformation is reported. Substitution of the cluster of hydrophobic residues with Ala decreases [k.sub.cat]/[K.sub.m] with a minimal effect on [k.sub.cat] provides evidence that the cluster stabilizes the closed conformation.

The article presents a new peptide-based nanoparticle system, which can be used for the siRNA delivery in different cell lines, CADY. The structural polymorphism is shown to be an extremely important factor that facilitates the CADY cellular membrane interactions.

Circular dichroism and UV resonance Raman spectroscopy was employed to study the impact of alcohols on the conformational equilibria and relative Gibbs free energy landscapes along the Ramachandran [Psi]-coordinate of a mainly poly-Ala peptide, AP with an AAAAA[(AAARA).sub.3]A sequence. Alcohols stabilized [pi]-bulge conformation more than the [alpha]-helix, while the [3.sub.10]-helix was destabilized due to the alcohol-increased hydrophobicity and 2,2,2-Trifluoroethanol (TFE) induced more [alpha]-helices, it favored multiple, shorter helix segments.

The effects of preventing or modifying the [[beta].sub.2] subunit N-glycosylation on trafficking of the subunit and its binding to the ER lectin chaperone, calnexin are examined to the study the role of N-glycans in maturation of the Na,K-ATPase [[beta].sub.2] subunit in the ER. The hydrophobic residues in the proximity of N-glycans 2 and 7 are required for post-translational calnexin binding to these N-glycans in incompletely folded conformers, which, in turn, is necessary for maturation of the Na,K-ATPase [[beta].sub.2] subunit.

The molecular dynamics (MD) simulations were performed for the fatty acid (FA) synthase intermediates [beta]-ketoacyl-, [beta]-hydroxyacyl, and trans-2-enoyl-Acyl carrier protein (ACP) spanning from 4 to 18 carbon groups in length to gain better insigth into their structures. The results for bindings kinetics of [beta]-ketoacyl and [beta]-hydroxyacyl chains provide insigth into the different acyl-ACP intermediates which migh be distinguished by FA synthase enzymes.

The three-dimensional structural characterization and dynamics of a central B domain (residues 73-200) and a C domain (residues 201-326) from the membrane protein Rv0899 (OmpATb) from Mycobacterium tuberculosis are described. Residues 73-326 are observed to form a mixed [alpha]/[beta]-globular structure, encompassing two independently folded modules corresponding to the B and C domains connected by a flexible linker.

The crystal structure characterization of cyanobacterial PsbQ isolated from Synechocystis sp. in presence and absence of [Zn.sup.2+] is described. The characterization identified the protein as a well-defined helical core, containing four helices arranged in an up-down-up-down fold and a conserved potential interaction site composed of a divalent metal binding site and adjacent hydrophobic pocket.

A study was conducted to identify core structural residues in the sequentially diverse and structurally homologous Bcl-2 family of proteins which regulates the intrinsic pathway of apoptosis and plays a significant role in mitochondrial outer membrane permeabilization. The study results could be applied for the genome-wide identification of hitherto unrecognized Bcl-2 family members, particularly in viral genomes.

A study was conducted to examine the effect of the single-residue mutation of leucine 42 to arginine (L42R) centrally positioned in the polypeptide binding pocket of SecB on its chaperonin function in Escherichia coli. The study results indicated that a reduced polypeptide binding affinity exhibited by SecB(L42R) mutant facilitated the partial folding of the bound polypeptide chain rendering it translocation-incompetent.

A genetic screening was conducted to identify mutants with a substitution at residue I174 that resulted in a mutator polymerase and understand the role of hinge residue I174 in polymerase fidelity. The results revealed that the hinge region is critical for the maintenance of the proper geometry of the dNTP binding pocket.

The solution structure of the norsolorinic acid synthase (NSAS) holo Acyl (peptidyl) carrier protein (ACP or PCP) domain excised from the full-length multifunctional enzyme is reported. The results confirmed the view that type I ACPs does not exhibit any significant affinity for hydrophobic (nonpolar) chain assembly intermediates attached via the 4'-phosphopantetheine prosthetic group.

Five hydrophobic residues in the regulatory domain of TnC were individually substituted with polar Gln to examine effect of mutations that sensitized isolated TnC to calcium. The results suggested that both, the intrinsic properties of TnC and its interactions with the other contractile proteins play a significant role in modulating the binding of calcium to TnC in increasingly complex biochemical systems.

The application of SUPREX (stability of unpurified proteins from rates of H-D exchange), an H-D exchange and MALDI-based technique is described in order to study the binding interaction between the molecular chaperone Hsp33 and four different unfolded protein substrates, such as citrate synthase, lactate dehydrogenase, malate dehydrogenase, and aldolase. The study results suggested that the cooperativity of the Hsp33 folding-unfolding reaction increases upon binding with denatured protein substrates.

Osmolyte cosolvents are utilized show that hydrogen-bonding contributions could be separated from hydrophobic interactions in the denatured state ensemble (DSE). Minor changes observed in the strength of hydrophobic interaction on transfer of DSE from 6 M urea to water and then to 1 M TMAO suggested that backbone-backbone (hydrogen-bonding) interactions are greatly enhanced due to progressively poorer solvent quality for the peptide backbone.

A study related to the single-domain cyclophilin 18 (Cyp18), known to function as a peptidyl-prolyl cis/trans isomerase (PPI) and also function as both a folding catalyst and a chaperone is presented. The chaperone effect of Cyp18 demonstrated for citrate synthase indicated a general chaperone effect of Cyp18 PPI.

The crystal structure characterization of human carbonic anhydrase II (HCA II) is obtained at 0.9 [Angstrom] resolution to reveal a water molecule, termed deep water, Dw, bound in a hydrophobic pocket of the active site that forms a short, strong hydrogen bond with the zinc-bound solvent molecule. The short, strong hydrogen bond formed is expected to contribute to the low p[K.sub.a] of the zinc-bound water and to promote proton transfer in catalysis.

Time-resolved photolabeling with the hydrophobic probe 3-(trifluoromethyl)-3-(m-iodophenyl)diazirine (TID) was used to monitor structural changes occurring during fast and slow desensitization in the transmembrane domain of the Torpedo nicotinic acetylcholine receptor (nAChR). Based on the results it was concluded that the local conformation is different in each state and is consistent with the hypothesis which suggest that there are separate gates for channel opening and desensitization.

NMR structural study is carried out to understand the conformational changes observed in the MDM2-binding region (residues S15 to N29 (SN15) peptide) in p53TAD upon binding to Bcl-[X.sub.L]. A Bcl-[X.sub.L]/SN15 complex structural model suggested that the SN15 peptide adopted an extended [alpha]-helical structure to bind to the hydrophobic pocket on the Bcl-[X.sub.L], which is similar to the mode of binding between BH3 peptides and Bcl-XL.

The interprotein electron transfer reaction between cytochrome [c.sub.2] (cyt) and the reaction center (RC) was explored to determine the mechanisms related to coupling association and electron transfer. The obtained results provide a quantitative model for coupling protein association with electron transfer and demonstrated the role of short-range interactions in determining the rate of electron transfer.

All-atom and coarse-grained (CG) molecular dynamics (MD) simulations of high-density lipoprotein (HDL) particles that have major implications for mechanisms of the enzyme lecithin:cholesterol acyltransferase (LCAT), cholesteryl ester (CE) activation is reported. After attachment of LCAT to discoidal HDL, the helix 5/5 domains in apoA-I is observed to form amphipathic presentation tunnels for migration of hydrophobic acyl chains and amphipathic unesterified cholesterol (UC) from the bilayer to the phospholipase A2-like and esterification active sites of LCAT, respectively.