Adenosine dialdehyde, a methyltransferase inhibitor, induces colorectal cancer cells apoptosis by regulating PIMT:p53 interaction.

Post-translational modification (PTM) is important in controlling many biological processes by changing the structure and function of a protein. Protein methylation is an important PTM, and the role of methyltransferases has been implicated in numerous cellular functions. Protein L-isoaspartyl methyltransferase (PIMT) is ubiquitously expressed in almost all organisms and govern important cellular processes including apoptosis. Among other functions, PIMT has also been identified as a potent oncogene because it destabilizes the structure of the tumor suppressor p53 via methylation at the transactivation domain. In the present study we identified that out of the three methyltransferase inhibitors tested, namely, S-adenosyl-l-homocysteine (AdoHcy), adenosine and adenosine dialdehyde (AdOx), only AdOx augments p53 expression by destabilizing PIMT structure, as evident from far-UV CD. The effect of the inhibitors, AdOx in particular, to the structure of PIMT, and the binding of PIMT to the p53 transactivation domain have been investigated by docking and molecular dynamics simulations. AdOx significantly increases p53 accumulation and nuclear translocation in colon cancer cells, triggering the p53-mediated apoptotic pathway. To better understand the molecular mechanisms underlying p53 accumulation in colon cancer cells, we observed that the level of PIMT is considerably lower in AdOx-treated cells, reducing its association with p53, which stabilized p53. p53 then transactivated BAX, increasing the BAX: BCL-2 ratio and causing colon cancer cell death.

On the pathway of the formation of secondary structures in proteins.

Protein structures are typically made up of well-defined modules, called secondary structures. A hierarchical model of protein folding may start with the formation of five-membered non-covalently-linked ring motifs involving O⋅⋅⋅C=O and N-H···N interactions connecting two consecutive peptide groups. Some of these interactions lead to polyproline II structure, which are known to occur in the unfolded state of proteins. These interactions constitute different types of γ-turns, providing the sharpest reversal of the chain direction. Occurring transiently in the unfolded state, and in tandem, they can lead to ß-turns. One of the ß-turns (type I) is predisposed (from a consideration of residue usage) to form the N-terminal of an α-helix, which then propagates toward its C-terminal direction. O⋅⋅⋅C=O interactions encompass four distinct types of conformational features, and one of them has very similar backbone torsion angles as the polyproline II (PPII) conformation and can thus contribute to the formation of PPII helix. An adjustment from these angles can also drive the formation of ß-strand. N-H···N interactions can also constitute capping interaction at helix termini and can link a PPII helix to an α-helix. Thus, the polypeptide backbone is endowed with all the features that can initiate the formation of secondary structural elements, and the γ-turn motifs (resulting from O⋅⋅⋅C=O and N-H···N interactions) are the basic units the protein structures are made up of.

The Role of Protein-L-isoaspartyl Methyltransferase (PIMT) in the Suppression of Toxicity of the Oligomeric Form of Aß42, in Addition to the Inhibition of Its Fibrillization.

The oligomeric form of amyloid-ß peptide (Aß42) plays a crucial role in the pathogenesis of Alzheimer's disease (AD) and is responsible for cognitive deficits. The soluble oligomers are believed to be more toxic compared to the fibril form. Protein-L-isoaspartyl methyltransferase (PIMT) is a repair enzyme that converts aberrant isoAsp residues, formed spontaneously on isomerization of normal Asp and Asn residues, back to typical Asp. It was shown to inhibit the fibrillization of Aß42 (containing three Asp residues), and here, we investigate its effect on the size, conformation, and toxicity of Aß42 oligomers (AßO). Far-UV CD indicated a shift in the conformational feature of AßOs from the random coil to ß-sheet in the presence of PIMT. Binding of bis-ANS to different AßOs (obtained using different concentrations of Aß42 monomer) indicated the correlation of size of oligomers to hydrophobicity: the smallest AßO having the highest hydrophobicity is the most toxic. Dynamic light scattering showed an increase in size of AßO with the addition of PIMT, a contrasting role to that on Aß fibril. Assays using PC12-derived neurons showed the neuroprotective role of PIMT against AßO-induced toxicity. Furthermore, we have elaborated on the molecular mechanism of the antifibrillar action of PIMT and how this function is correlated with its enzymatic activity. PIMT has a more pronounced effect on AßO as compared to a small heat shock protein, pointing to its importance for the amelioration of the adverse effect of both Aß42 oligomers and fibrils.

Antimicrobial potential of a ponericin-like peptide isolated from Bombyx mori L. hemolymph in response to Pseudomonas aeruginosa infection.

The main effectors in the innate immune system of Bombyx mori L. are antimicrobial peptides (AMPs). Here, we infected B. mori with varied inoculum sizes of Pseudomonas aeruginosa ATCC 25668 cells to investigate changes in morpho-anatomical responses, physiological processes and AMP production. Ultraviolet-visible spectra revealed a sharp change in λmax from 278 to 285 nm (bathochromic shift) in the hemolymph of infected B. mori incubated for 24 h. Further, Fourier Transform InfraRed studies on the hemolymph extracted from the infected B. mori showed a peak at 1550 cm-1, indicating the presence of α-helical peptides. The peptide fraction was obtained through methanol, acetic acid and water mixture (90:1:9) extraction, followed by peptide purification using Reverse Phase High Performance Liquid Chromatography. The fraction exhibiting antibacterial properties was collected and characterized by Matrix-Assisted Laser Desorption/Ionization-Time of Flight. A linear α-helical peptide with flexible termini (LLKELWTKMKGAGKAVLGKIKGLL) was found, corresponding to a previously described peptide from ant venom and here denominated as Bm-ponericin-L1. The antibacterial activity of Bm-ponericin-L1 was determined against ESKAPE pathogens. Scanning electron microscopy confirmed the membrane disruption potential of Bm-ponericin-L1. Moreover, this peptide also showed promising antibiofilm activity. Finally, cell viability and hemolytic assays revealed that Bm-ponericin-L1 is non-toxic toward primary fibroblasts cell lines and red blood cells, respectively. This study opens up new perspectives toward an alternative approach to overcoming multiple-antibiotic-resistance by means of AMPs through invertebrates' infection with human pathogenic bacteria.

ProDFace: A web-tool for the dissection of protein-DNA interfaces.

Protein-DNA interactions play a crucial role in gene expression and regulation. Identifying the DNA binding surface of proteins has long been a challenge-in comparison to protein-protein interactions, limited progress has been made in the development of efficient DNA binding site prediction and protein-DNA docking methods. Here we present ProDFace, a web tool that characterizes the binding region of a protein-DNA complex based on amino acid propensity, hydrogen bond (HB) donor capacity (number of solvent accessible HB donor groups), sequence conservation at the interface core and rim region, and geometry. The program takes as input the structure of a protein-DNA complex in PDB (Protein Data Bank) format, and outputs various physicochemical and geometric parameters of the interface, as well as conservation of the interface residues in the protein component. Values are provided for the whole interface, and after dissecting it into core and rim regions. Details of water mediated HBs between protein and DNA, potential HB donor groups present at the binding surface of protein, and conserved interface residues are also provided as downloadable text files. These parameters can be useful in evaluating and validating protein-DNA docking solutions, structures derived from simulation as well as solutions from the available prediction tools, and facilitate the development of more efficient prediction methods. The web-tool is freely available at structbioinfo.iitj.ac.in/resources/bioinfo/pd_interface .

Intrinsically disordered proteins/regions and insight into their biomolecular interactions.

Proteins may vary from being rigid to having flexible regions to being completely disordered, either as an intrinsically disordered protein (IDP) or having specific intrinsically disordered regions (IDRs). IDPs/IDRs can form complexes otherwise impossible, such as wrapping around the binding partner, hence providing the plasticity needed for achieving assemblies with specific functions. IDRs can exhibit promiscuity, using the same region in the sequence to bind multiple partners, and act as hubs in protein-protein interaction network (an essential part of the cell signalling network). Disorder-to-order transition on binding provides specificity with affinity, optimum for reversibility of the binding, thus offering suitability for regulation and signalling processes. IDRs interactions may be modulated by the environment or covalent modifications; mis-signalling or their unnatural or non-native folding may lead to diseases. This article aims to provide an overview of structural heterogeneity, as seen in IDPs/IDRs, and their role in biological recognition, binding and function.

O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding.

Various noncovalent interactions, long and short range, stabilize the native protein structure. We had observed a short-range interaction between two adjacent peptide groups in a nearly perpendicular orientation through the involvement of an NH‧‧‧N hydrogen bond. Here we show that the other half of the peptide group, namely the carbonyl moiety, can also be involved through the O‧‧‧C═O interaction. Considering the interacting residues, the second residue of the pair has distinct backbone conformational angles, occurring in four clusters, each engendering well-defined structural motifs. One of the motifs is the γ-turn, another being polyproline II helix. The interacting pair is found mostly in the irregular region in protein structures, and the propensities of residues and the identification of the nearest secondary structure show interesting patterns. The most conspicuous ß-turn conformation is built from two consecutive γ-turns, with embedded O‧‧‧C═O and NH‧‧‧N interactions, and there is considerable match of the residue usage at the central positions of the ß-turn and the γ-turn components. This clearly exemplifies the hierarchical growth of the protein secondary structures, which would be important in our understanding of protein folding. While the occurrence of the O‧‧‧C═O interaction in α-helices has been well documented, we find it to be equally important in making capping interactions at helix termini.

Effect of gold nanoparticles on the structure and neuroprotective function of protein L-isoaspartyl methyltransferase (PIMT).

Fibrillation of peptides and proteins is implicated in various neurodegenerative diseases and is a global concern. Aging leads to the formation of abnormal isoaspartate (isoAsp) residues from isomerization of normal aspartates in proteins, triggering fibril formation that leads to neurodegenerative diseases. Protein L-isoaspartyl methyltransferase (PIMT) is a repair enzyme which recognizes and converts altered isoAsp residues back to normal aspartate. Here we report the effect of gold nanoparticles (AuNPs) of different sizes on the structure and function of PIMT. Spherical AuNPs, viz. AuNS5, AuNS50 and AuNS100 (the number indicating the diameter in nm) stabilize PIMT, with AuNS100 exhibiting the best efficacy, as evident from various biophysical experiments. Isothermal titration calorimetry (ITC) revealed endothermic, but entropy driven mode of binding of PIMT with all the three AuNSs. Methyltransferase activity assay showed enhanced activity of PIMT in presence of all AuNSs, the maximum being with AuNS100. The efficacy of PIMT in presence of AuNS100 was further demonstrated by the reduction of fibrillation of Aß42, the peptide that is implicated in Alzheimer's disease. The enhancement of anti-fibrillation activity of PIMT with AuNS100 was confirmed from cell survival assay with PC12 derived neuronal cells against Aß42 induced neurotoxicity.

The gold nanoparticle reduces Vibrio cholerae pathogenesis by inhibition of biofilm formation and disruption of the production and structure of cholera toxin.

Formation of biofilm by Vibrio cholerae plays a crucial role in pathogenesis and transmission of cholera. Lower infective dose of the biofilm form of V. cholerae compared to the planktonic counterpart, and its antibiotic resistance, make it challenging to combat cholera. Nanoparticles may serve as an effective alternative to conventional antibiotics for targeting biofilms and virulence factors. We explored the effectiveness of gold nanoparticles (AuNPs) of different size and shape (spherical: AuNS10 and AuNS100, and rod: AuNR10, the number indicating the diameter in nm) on both the inhibition of formation and eradication of biofilm of the two biotypes of V. cholerae, classical (VcO395) and El Tor (VcN16961). Inhibition of biofilm formation by spherical AuNPs was observed for both the biotypes. Considering eradication, the biofilms for both, particularly El Tor, was destroyed using both the AuNSs, AuNS100 showing higher efficacy. AuNR10 did not affect the biofilm of either biotype. Micrographs of small intestinal sections of VcO395-infected mice indicated the inhibition of biofilm formation by both AuNSs. We also studied the effect of these AuNPs on the structure of cholera toxin (CT), the major toxin produced by V. cholerae. Far-UV CD showed both AuNR10 and AuNS100 compromised the structure of CT, which was also validated from the reduction of fluid accumulation in mice ileal loop. Western blot analysis revealed the reduction of CT production upon treatment with AuNPs. AuNS100 seems to be the best suited to inhibit the formation or destruction of biofilm, as well as to disrupt CT production and function.

RGS5-TGFß-Smad2/3 axis switches pro- to anti-apoptotic signaling in tumor-residing pericytes, assisting tumor growth.

Regulator-of-G-protein-signaling-5 (RGS5), a pro-apoptotic/anti-proliferative protein, is a signature molecule of tumor-associated pericytes, highly expressed in several cancers, and is associated with tumor growth and poor prognosis. Surprisingly, despite the negative influence of intrinsic RGS5 expression on pericyte survival, RGS5highpericytes accumulate in progressively growing tumors. However, responsible factor(s) and altered-pathway(s) are yet to report. RGS5 binds with Gαi/q and promotes pericyte apoptosis in vitro, subsequently blocking GPCR-downstream PI3K-AKT signaling leading to Bcl2 downregulation and promotion of PUMA-p53-Bax-mediated mitochondrial damage. However, within tumor microenvironment (TME), TGFß appeared to limit the cytocidal action of RGS5 in tumor-residing RGS5highpericytes. We observed that in the presence of high RGS5 concentrations, TGFß-TGFßR interactions in the tumor-associated pericytes lead to the promotion of pSmad2-RGS5 binding and nuclear trafficking of RGS5, which coordinately suppressed RGS5-Gαi/q and pSmad2/3-Smad4 pairing. The RGS5-TGFß-pSmad2 axis thus mitigates both RGS5- and TGFß-dependent cellular apoptosis, resulting in sustained pericyte survival/expansion within the TME by rescuing PI3K-AKT signaling and preventing mitochondrial damage and caspase activation. This study reports a novel mechanism by which TGFß fortifies and promotes survival of tumor pericytes by switching pro- to anti-apoptotic RGS5 signaling in TME. Understanding this altered RGS5 signaling might prove beneficial in designing future cancer therapy.

Inhibition of microtubule assembly and cytotoxic effect of graphene oxide on human colorectal carcinoma cell HCT116.

Nanomaterials, such as graphene oxide (GO), are increasingly being investigated for their suitability in biomedical applications. Tubulin is the key molecule for the formation of microtubules crucial for cellular function and proliferation, and as such an appealing target for developing anticancer drug. Here we employ biophysical techniques to study the effect of GO on tubulin structure and how the changes affect the tubulin/microtubule assembly. GO disrupts the structural integrity of the protein, with consequent retardation of tubulin polymerization. Investigating the anticancer potential of GO, we found that it is more toxic to human colon cancer cells (HCT116), as compared to human embryonic kidney epithelial cells (HEK293). Immunocytochemistry indicated the disruption of microtubule assembly in HCT116 cells. GO arrested cells in the S phase with increased accumulation in Sub-G1 population of cell cycle, inducing apoptosis by generating reactive oxygen species (ROS) in a dose- and time-dependent manner. GO inhibited microtubule formation by intervening into the polymerization of tubulin heterodimers both in vitro and ex vivo, resulting in growth arrest at the S phase and ROS induced apoptosis of HCT116 colorectal carcinoma cells. There was no significant harm to the HEK293 kidney epithelial cells used as control. Our report of pristine GO causing ROS-induced apoptosis of cancer cells and inhibition of tubulin-microtubule assembly can be of interest in cancer therapeutics and nanomedicine.

Virstatin-Conjugated Gold Nanoparticle with Enhanced Antimicrobial Activity against the Vibrio cholerae El Tor Biotype.

Because of the emergence of multidrug-resistant pathogenic bacteria, there is a growing interest for the development of an efficient alternative to antibiotics. Gold nanoparticles (AuNPs) are promising candidates due to their inherent non-toxicity and can be used as effective carriers of drugs. Cholera caused by Gram-negative Vibrio cholerae is still a potential threat in many developing countries. Virstatin, a small molecule, has been reported to inhibit virulence regulation in V. cholerae. Herein, we report an efficient synthesis of virstatin-conjugated gold nanoparticles (VL-AuNPs) and their antibacterial efficacy against the El Tor biotype of V. cholerae (VcN16961). The spherical-shaped NPs have an average diameter of ∼17 nm. The uniqueness of VL-AuNPs relies in the enhanced antibacterial efficacy compared to virstatin, as evidenced from the inhibitory concentration obtained from growth kinetics, and attributed to the inhibition of ATPase activity and DNA damage. More importantly, the expression of cholera toxin, the most important virulence factor of V. cholera, is reduced to a far greater extent than by any of the component molecules. The effect of VL-AuNPs on VcN16961 was monitored using various assays such as confocal microscopy, FACS, fluorescence spectroscopy, and so on. Overall, VL-AuNPs could be a potential candidate for the use as an effective agent for combating diarrheal diseases caused by V. cholera.

The susceptibility of disulfide bonds towards radiation damage may be explained by S⋯O interactions.

Radiation-induced damage to protein crystals during X-ray diffraction data collection is a major impediment to obtaining accurate structural information on macromolecules. Some of the specific impairments that are inflicted upon highly brilliant X-ray irradiation are metal-ion reduction, disulfide-bond cleavage and a loss of the integrity of the carboxyl groups of acidic residues. With respect to disulfide-bond reduction, previous results have indicated that not all disulfide bridges are equally susceptible to damage. A careful analysis of the chemical environment of disulfide bonds in the structures of elastase, lysozyme, acetylcholinesterase and other proteins suggests that S-S bonds which engage in a close contact with a carbonyl O atom along the extension of the S-S bond vector are more susceptible to reduction than the others. Such an arrangement predisposes electron transfer to occur from the O atom to the disulfide bond, leading to its reduction. The interaction between a nucleophile and an electrophile, akin to hydrogen bonding, stabilizes protein structures, but it also provides a pathway of electron transfer to the S-S bond, leading to its reduction during exposure of the protein crystal to an intense X-ray beam. An otherwise stabilizing interaction can thus be the cause of destabilization under the condition of radiation exposure.

Delineation of a new structural motif involving NHN γ-turn.

Macromolecules are characterized by distinctive arrangement of hydrogen bonds. Different patterns of hydrogen bonds give rise to distinct and stable structural motifs. An analysis of 4114 non-redundant protein chains reveals the existence of a three-residue, (i - 1) to (i + 1), structural motif, having two hydrogen-bonded five-membered pseudo rings (the first, an NH···OC involving the first residue, and the second being NH∙∙∙N involving the last two residues), separated by a peptide bond. There could be an additional hydrogen bond between the side-chain at (i-1) and the main-chain NH of (i + 1). The average backbone torsion angles of -76(±21)° and - 12(±17)° at i creates a tight turn in the polypeptide chain, akin to a γ-turn. Indeed, a search of three-residue fragments with restriction on the terminal Cα ···Cα distance and the existence of the two pseudo rings on either side revealed the presence 14 846 cases of a variant, termed NHN γ-turn, distinct from the NHO γ-turn (2032 cases) that has traditionally been characterized by the presence of NHO hydrogen bond linking the terminal main-chain atoms. As in the latter, the newly identified γ-turns are also of two types-classical and inverse, occurring in the ratio of 1:6. The propensities of residues to occur in these turns and their secondary structural features have been enumerated. An understanding of these turns would be useful for structure prediction and loop modeling, and may serve as models to represent some of the unfolded state or disordered region in proteins.

The role of isoaspartate in fibrillation and its prevention by Protein-L-isoaspartyl methyltransferase.

BACKGROUND: Isomerization of aspartate to isoaspartate (isoAsp) on aging causes protein damage and malfunction. Protein-L-isoaspartyl methyltransferase (PIMT) performs a neuroprotective role by repairing such residues. A hexapeptide, Val-Tyr-Pro-(isoAsp)-His-Ala (VA6), a substrate of PIMT, is shown to form fibrils, while the normal Asp-containing peptide does not. Considering the role of PIMT against epileptic seizure, the combined effect of PIMT and two antiepileptic drugs (AEDs) (valproic acid and stiripentol) was investigated for anti-fibrillation activity. METHODS: Structural/functional modulations due to the binding of AEDs to PIMT were investigated using biophysical techniques. Thioflavin T (ThT) fluorescence assay and microscopic methods were employed to study fibril formation by VA6. In vitro experiments with PC12 cells were carried out with PIMT/AEDs. RESULTS: ThT assay indicated reduction of fibrillation of VA6 by PIMT. AEDs stabilize PIMT, bind close to the cofactor binding site, possibly exerting allosteric effect, increase the enzymatic activity, and anti-fibrillation efficacy. Furthermore, Aß42, implicated in Alzheimer's disease, undergoes ß-sheet to α-helix transition in presence of PIMT. Studies with PC12 derived neurons showed that PIMT and PIMT/AEDs exerted neuroprotective effect against anti-NGF induced neurotoxicity. This was further validated against neurotoxicity induced by Aß42 in primary rat cortical neurons. CONCLUSIONS: The study provides a new perspective to the role isoAsp in protein fibrillation, PIMT in its prevention and AEDs in enhancing the activity of the enzyme. GENERAL SIGNIFICANCE: IsoAsp, with an additional C atom in the main-chain of polypeptide chain, may make it more susceptible to fibrillation. PIMT alone, or in association with AEDs prevents this.

Self-Assembly of Ferritin: Structure, Biological Function and Potential Applications in Nanotechnology.

Protein cages are normally formed by the self-assembly of multiple protein subunits and ferritin is a typical example of a protein cage structure. Ferritin is a ubiquitous multi-subunit iron storage protein formed by 24 polypeptide chains that self-assemble into a hollow, roughly spherical protein cage. Ferritin has external and internal diameters of approximately 12 nm and 8 nm, respectively. Functionally, ferritin performs iron sequestration and is highly conserved in evolution. The interior cavity of ferritin provides a unique reaction vessel to carry out reactions separated from the exterior environment. In nature, the cavity is utilized for sequestration of iron and bio-mineralization as a mechanism to render iron inert and safe from the external environment. Material scientists have been inspired by this system and exploited a range of ferritin superfamily proteins as supramolecular templates to encapsulate different carrier molecules ranging from cancer drugs to therapeutic proteins, in addition to using ferritin proteins as well-defined building blocks for fabrication. Besides the interior cavity, the exterior surface and sub-unit interface of ferritin can be modified without affecting ferritin assembly.

The antibacterial and anticancer properties of zinc oxide coated iron oxide nanotextured composites.

Core-shell α-Fe2O3-ZnO structures of different nanotextured morphology were synthesized through wet chemical routes using different solvents like ethanol, ethanolamine, water and acetaldehyde. Morphological tuning using different solvents resulted in the formation of different shapes, such as disc, spindle, rod and sphere (abbreviated as FZ-ND, FZ-NSP, FZ-NR and FZ-NS, respectively). Structural, morphological and compositional characterization of these nanoparticles (NPs) has been carried out. Antibacterial efficacy of the synthesized NPs was checked against Gram negative V. cholerae N16961 (VcN16961) and Gram positive S. aureus bacteria by recording optical density (OD) at different time points. Among the NPs tested, FZ-NSP was found to be the most effective against VcN16961, while FZ-NR showed maximum efficacy against S. aureus, implying the importance of nanotextured surface as well as the morphology in the manifestation of antibacterial activity. The kinetics of growth for both the bacteria has been modelled using logistic approach. Cytotoxicity was evaluated through MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyltetrazolium bromide) assay against human breast adenocarcinoma cell line (MCF-7), human hepatocarcinoma cell line (HepG2) and against normal human embryonic kidney cell line (HEK-293). The lesser toxicity of α-Fe2O3-ZnO towards HEK-293 and the potent anticancer activity against MCF-7 and HepG2 cells underline its applicability as anticancer agent. With continued improvement of nanotechnology, this study may pave the way for designing and construction of various morphologically diverse, nanotextured materials with desired functional attributes.

Molecular features of interaction involving hen egg white lysozyme immobilized on graphene oxide and the effect on activity.

Nanomaterials, such as graphene oxide (GO) are being studied to decipher their suitability in biomedical applications. This study investigate the effect on structure and function of hen egg white lysozyme (HEWL) adsorbed on GO, using various biophysical techniques. In spite of there being not much change in the structure, the catalytic activity is reduced significantly. Fluorescence quenching indicates complex formation. Fluorescence lifetime measurement suggests that GO binds at or near the active site close to Trp62 and Trp108. Heat change associated with HEWL-GO interaction suggests hydrogen bond along with van der Waals and electrostatic interactions are involved in the HEWL-GO complex. Molecular docking indicates binding of GO at the active site corroborating experimental findings. Molecular dynamics simulations indicate that the blocking of the active site affects the flexibility of the surrounding residues and contribute to the reduction of the activity. Unfolding experiments indicate that HEWL is more prone to thermal instability in presence of GO. Together, the results obtained established molecular details of HEWL-GO interaction and might be useful in eventual biomedical applications of GO.

Structural motif, topi and its role in protein function and fibrillation.

A protein chain is arranged into regions in which the backbone is organized into regular patterns (of conformation and hydrogen bonding) to form the most common secondary structures, α-helix and ß-sheet, which are interspersed by turns and more irregular loop regions. A structural motif, topi, is discussed in which a pair of 2-residue segments, each containing hydrogen-bonded five-membered fused-ring motifs, distant in sequence are linked to each other by a hydrogen bond. Though a small motif, it appears to be important in the context of local folding patterns of proteins and occurs near protein active sites. The motif shows quite significant residue preference, and a Cys (or Ser) occupying the second position may further stabilize the motif by forming an additional hydrogen bond across it. Remarkably, topi is found within disease causing misfolded proteins, such as the fibrilled form of Aß42, and also across the interface between two protein chains. This motif may be an important component of fibrillation and useful for modeling loop regions.

Structural changes in DNA-binding proteins on complexation.

Characterization and prediction of the DNA-biding regions in proteins are essential for our understanding of how proteins recognize/bind DNA. We analyze the unbound (U) and the bound (B) forms of proteins from the protein-DNA docking benchmark that contains 66 binary protein-DNA complexes along with their unbound counterparts. Proteins binding DNA undergo greater structural changes on complexation (in particular, those in the enzyme category) than those involved in protein-protein interactions (PPI). While interface atoms involved in PPI exhibit an increase in their solvent-accessible surface area (ASA) in the bound form in the majority of the cases compared to the unbound interface, protein-DNA interactions indicate increase and decrease in equal measure. In 25% structures, the U form has missing residues which are located in the interface in the B form. The missing atoms contribute more toward the buried surface area compared to other interface atoms. Lys, Gly and Arg are prominent in disordered segments that get ordered in the interface on complexation. In going from U to B, there may be an increase in coil and helical content at the expense of turns and strands. Consideration of flexibility cannot distinguish the interface residues from the surface residues in the U form.