An automated approach to network features of protein structure ensembles

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of 2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

Carbohydrate-Appended Tumor Targeting Iron(III) Complexes Showing Photocytotoxicity in Red Light

Glucose-appended photocytotoxic iron(III) complexes of a tridentate Schiff base phenolate ligand Fe(bpyag) (L)] (NO3) (1-3), where bpyag is N,N-bis(2- pyridylmethyl)-2-aminoethyl-beta-D-glucopyranoside and H2L is 3-(2-hydroxyphenylimino)-1-phenylbutan-1-one (H(2)phap) in 1, 3-(2-hydroxyphenylimino)-9-anthrylbutan-1-one (H(2)anap) 2, and 3- (2-hydroxyphenylimino)-1-pyrenylbutan-1-one (H(2)pyap) in 3, were synthesized and characterized. The complex Fe(dpma)(anapn(NO3) (4), having bis-(2-pyridylmethyl)benzylamine (dpma), in which the glucose moiety of bpyag is substituted by a phenyl group, was used as a control, and the complex Fe(dpma)(anap)](PF6) (4a) was structurally characterized by X-ray crystallography. The structure shows a FeN4O2 core in a distorted octahedral geometry. The high-spin iron(III) complexes with magnetic moment value of similar to 5.9 mu(B) showed a low-energy phenolate-to-Fe(III) charge-transfer (CT) absorption band as a shoulder near 500 nm with a tail extending to 700 nm and an irreversible Fe(III)-Fe(II) redox couple near -0.6 V versus saturated calomel electrode. The complexes are avid binders to calf thymus DNA and showed photocleavage of supercoiled pUC19 DNA in red (647 nm) and green (532 nm) light. Complexes 2 and 3 displayed significant photocytotoxicity in red light, with an IC50 value of similar to 20 mu M in HeLa and HaCaT cells, and no significant toxicity in dark. The cell death is via an apoptotic pathway, by generation of reactive oxygen species. Preferential internalization of the carbohydrate-appended complexes 2 and 3 was evidenced in HeLa cells as compared to the control complex 4. A 5-fold increase in the cellular uptake was observed for the active complexes in HeLa cells. The photophysical properties of the complexes are rationalized from the density functional theory calculations.

TSpred: a web server for the rational design of temperature-sensitive mutants

Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes.

Effect of metal oxidation state on FRET: a Cu(I) silent but selectively Cu(II) responsive fluorescent reporter and its bioimaging applications

Copper(II) and copper(I) complexes of a newly designed and crystallographically characterized Schiff base (HL) derived from rhodamine hydrazide and cinnamaldehyde were isolated in pure form formulated as Cu(L)(NO3)] (L-Cu) (1) and Cu(HL)(CH3CN)(H2O)]ClO4 (HL-Cu) (2), and characterized by physicochemical and spectroscopic tools. Interestingly, complex 1 but not 2 offers red fluorescence in solution state, and eventually HL behaves as a Cu(II) ions selective FRET based fluorosensor in HEPES buffer (1 mM, acetonitrile-water: 1/5, v/v) at 25 degrees C at biological pH with almost no interference of other competitive ions. The dependency of the FRET process on the +2 oxidation state of copper has been nicely supported by exhaustive experimental studies comprising electronic, fluorimetric, NMR titration, and theoretical calculations. The sensing ability of HL has been evaluated by the LOD value towards Cu(II) ions (83.7 nM) and short responsive time (5-10 s). Even the discrimination of copper(I) and copper(II) has also been done using only UV-Vis spectroscopic study. The efficacy of this bio-friendly probe has been determined by employing HL to detect the intercellular distribution of Cu(II) ions in HeLa cells by developing image under fluorescence microscope.

Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity

Jacalin is among the most thoroughly studied lectins. Its carbohydrate-binding site has also been well characterized. It has been postulated that the lower affinity of beta-galactosides for jacalin compared with beta-galactosides is caused by steric interactions of the substituents in the former with the protein. This issue has been explored energetically and structurally using different appropriate carbohydrate complexes of jacalin. It turns out that the earlier postulation is not correct. The interactions of the substituent with the binding site remain essentially the same irrespective of the anomeric nature of the substitution. This is achieved through a distortion of the sugar ring in beta-galactosides. The difference in energy, and therefore in affinity, is caused by a distortion of the sugar ring in beta-galactosides. The elucidation of this unprecedented distortion of the ligand as a strategy for modulating affinity is of general interest. The crystal structures also provide a rationale for the relative affinities of the different carbohydrate ligands for jacalin.

Remarkable Selectivity and Photo-Cytotoxicity of an Oxidovanadium(IV) Complex of Curcumin in Visible Light

Oxidovanadium(IV) complexes of 2-(2'-pyridyl)-1,10-phenanthroline (pyphen), viz. VO(pyphen)(acac)](ClO4) (1), VO(pyphen)(anacac)](ClO4) (2) and VO(pyphen)(cur)](ClO4) (3), where acac is acetylacetonate (in 1), anacac is anthracenylacetylacetonate (in 2) and cur is curcumin monoanion (in 3) were synthesized, characterized and their photo-induced DNA cleavage activities and photo-cytotoxicities studied. The complexes are 1: 1 electrolytes in DMF. The one-electron paramagnetic complexes show a d-d band near 760 nm in DMF. Complexes 2 and 3 are blue and green emissive, respectively, in DMSO. The complexes exhibit irreversible V-IV/V-III reductive responses near -1.1 V and V-V/V-IV oxidative responses near 0.85 V vs. SCE in DMF-0.1 M TBAP. Complexes 2 and 3 display significant and selective photo-cytotoxicity upon irradiation with visible light giving an IC50 value of about 5 mu M against HeLa and MCF-7 cancer cells; they are significantly less-toxic against normal 3T3 control cells and in the absence of light. Complex 1 was used as a control. Both cytosolic and nuclear localization of the complexes were observed on the basis of fluorescence imaging. The complexes, avid binders to calf thymus (ct) DNA, were found to photocleave supercoiled pUC19 DNA upon irradiation with near-IR light (785 nm) by generating hydroxyl radical (OH) as the reactive oxygen species (ROS). Cell death events noted with HeLa and MCF-7 cell lines likely are attributable to apoptotic pathways involving light-assisted generation of intracellular ROS.

Remarkable enhancement in photocytotoxicity and hydrolytic stability of curcumin on binding to an oxovanadium(IV) moiety

Oxovanadium(IV) complexes of polypyridyl and curcumin-based ligands, viz. VO(cur)(L)Cl] (1, 2) and VO(scur)(L)Cl] (3, 4), where L is 1,10-phenanthroline (phen in 1 and 3), dipyrido3,2-a:2',3'-c]phenazine (dppz in 2 and 4), Hcur is curcumin and Hscur is diglucosylcurcumin, were synthesized and characterized and their cellular uptake, photocytotoxicity, intracellular localization, DNA binding, and DNA photo-cleavage activity studied. Complex VO(cur)(phen)Cl] (1) has (VN2O3Cl)-N-IV distorted octahedral geometry as evidenced from its crystal structure. The sugar appended complexes show significantly higher uptake into the cancer cells compared to their normal analogues. The complexes are remarkably photocytotoxic in visible light (400-700 nm) giving an IC50 value of <5 mu M in HeLa, HaCaT and MCF-7 cells with no significant dark toxicity. The green emission of the complexes was used for cellular imaging. Predominant cytosolic localization of the complexes 1-4 to a lesser extent into the nucleus was evidenced from confocal imaging. The complexes as strong binders of calf thymus DNA displayed photocleavage of supercoiled pUC19 DNA in red light by generating (OH)-O-center dot radicals as the ROS. The cell death is via an apoptotic pathway involving the ROS. Binding to the VO2+ moiety has resulted in stability against any hydrolytic degradation of curcumin along with an enhancement of its photocytotoxicity.

Unusually Short Chalcogen Bonds Involving Organoselenium: Insights into the Se-N Bond Cleavage Mechanism of the Antioxidant Ebselen and Analogues

Structural studies on the polymorphs of the organoselenium antioxidant ebselen and its derivative show the potential of organic selenium to form unusually short Se center dot center dot center dot O chalcogen bonds that lead to conserved supramolecular recognition units. Se center dot center dot center dot O interactions observed in these polymorphs are the shortest such chalcogen bonds known for organoselenium compounds. The FTIR spectral evolution characteristics of this interaction from solution state to solid crystalline state further validates the robustness of this class of supramolecular recognition units. The strength and electronic nature of the Se center dot center dot center dot O chalcogen bonds were explored using high-resolution X-ray charge density analysis and atons-in-molecules (AIM) theoretical analysis. A charge density study unravels the strong electrostatic nature of Se center dot center dot center dot O chalcogen bonding and soft-metal-like behavior of organoselenium. An analysis of the charge density around Se-N and Se-C covalent bonds in conjunction with the Se center dot center dot center dot O chalcogen bonding modes in ebselen and its analogues provides insights into the mechanism of drug action in this class of organoselenium antioxidants. The potential role of the intermolecular Se center dot center dot center dot O chalcogen bonding in forming the intermediate supramolecular assembly that leads to the bond cleavage mechanism has been proposed in terms of electron density topological parameters in a series of molecular complexes of ebselen with reactive oxygen species (ROS).

``Conformational Simulation'' of Sulfamethizole by Molecular Complexation and Insights from Charge Density Analysis: Role of Intramolecular S center dot center dot center dot O Chalcogen Bonding

Intramolecular S center dot center dot center dot O chalcogen bonding and its potential to lock molecular conformation have been examined in the crystal forms of sulfamethizole, a sulfonamide antibiotic. Molecular complexes of sulfamethizole, including salts and cocrystal, have been synthesized, and their crystal structures were analyzed in order to examine the possible conformational preferences of the molecule in various ionic states and supramolecular environments (neutral/cocrystal, anionic salt, and cationic salt forms). The electrostatic potential mapped on Hirshfeld surfaces generated for these crystal forms provides insights into the possible binding modes of the drug in different environments. Further, the observed conformation locking feature has been rationalized in terms of the experimental charge density features of the intramolecular S center dot center dot O chalcogen bonding in sulfamethizole. The study quantitatively illustrates and rationalizes an intriguing case of a local minimum of molecular conformation being exclusively preferred over the global minimum, as it facilitates more efficient intermolecular interactions in a supramolecular environment.

Polypyridyl iron(II) complexes showing remarkable photocytotoxicity in visible light

Iron(II) complexes of polypyridyl ligands (B), viz. Fe(B)(2)]Cl-2 (1 and 2) of N, N, N-donor 2-(2-pyridyl)-1,10-phenanthroline (pyphen in 1) and 3-(pyridin-2-yl)dipyrido3,2-a:2',3'-c]phenazine (pydppz in 2), are prepared and characterized. They are 1:2 electrolytes in aqueous DMF. The diamagnetic complexes exhibit metal to ligand charge transfer band near 570 nm in DMF. The complexes are avid binders to calf thymus DNA giving binding constant (K (b)) values of similar to 10(6) M-1 suggesting significant intercalative DNA binding of the complexes due to presence of planar phenanthroline bases. Complex 2 exhibits significant photocytotoxicity in immortalized human keratinocyte cells HaCaT and breast cancer cell line MCF-7 giving IC50 values of 0.08 and 13 mu M in visible light (400-700 nm). Complex 2 shows only minor dark toxicity in HaCaT cells but is non-toxic in dark in MCF-7 cancer cells. The light-induced cellular damage follows apoptotic pathway on generation of reactive oxygen species as evidenced from the dichlorofluorescein diacetate (DCFDA) assay.

Endoplasmic reticulum targeting tumour selective photocytotoxic oxovanadium(IV) complexes having vitamin-B6 and acridinyl moieties

Oxovanadium(IV) complexes of vitamin-B6 Schiff base, viz., VO(HL1/L-2/L-3)(B)] Cl (1-4), where B is 2,2'-bipyridine (bpy in 1 and 2), 11-(9-acridinyl)dipyrido3,2-a:2',3'-c]phenazine (acdppz in 3 and 4), H2L1 center dot HCl is 3-hydroxy-5-(hydroxymethyl)-4-(((2-hydroxyphenyl)imino)methyl)-2-methylp yridin-1-ium chloride (in 1 and 4), HL2 is 2-(((2-(1H-imidazol-4-yl)ethyl) imino)methyl) phenol (in 2) and HL3 is 4-(((2-(1H-imidazol-4- yl)ethyl)imino)methyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol (in 3) were synthesized, characterized and their cellular uptake, photo-activated cytotoxicity and intracellular localization were studied. Complexes 1a, as the perchlorate salt of 1, and 2a, as the hexafluorophosphate salt of 2, were structurally characterized. Vitamin-B6 transporting membrane carrier (VTC) mediated entry into tumour cells in preference to the normal ones seems to be responsible for the higher cellular uptake of the complexes into HeLa and MCF-7 cells over MCF-10A cells. Complexes 3 and 4 having acdppz as the photosensitizer exhibit remarkable photocytotoxicity in these cancer cells giving IC50 of < 0.9 mu M. The complexes remain non-toxic in the dark. The complexes show photo-induced apoptotic cell death via singlet oxygen (O-1(2)) generation. Fluorescence microscopy reveals specific localization of complex 4 to endoplasmic reticulum (ER) and generation of O-1(2) possibly leads to apoptotic cell death by triggering ER stress response (ERSR).

Endoplasmic reticulum targeting tumour selective photocytotoxic oxovanadium(IV) complexes having vitamin-B6 and acridinyl moieties

Oxovanadium(IV) complexes of vitamin-B6 Schiff base, viz., VO(HL1/L-2/L-3)(B)] Cl (1-4), where B is 2,2'-bipyridine (bpy in 1 and 2), 11-(9-acridinyl)dipyrido3,2-a:2',3'-c]phenazine (acdppz in 3 and 4), H2L1 center dot HCl is 3-hydroxy-5-(hydroxymethyl)-4-(((2-hydroxyphenyl)imino)methyl)-2-methylp yridin-1-ium chloride (in 1 and 4), HL2 is 2-(((2-(1H-imidazol-4-yl)ethyl) imino)methyl) phenol (in 2) and HL3 is 4-(((2-(1H-imidazol-4- yl)ethyl)imino)methyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol (in 3) were synthesized, characterized and their cellular uptake, photo-activated cytotoxicity and intracellular localization were studied. Complexes 1a, as the perchlorate salt of 1, and 2a, as the hexafluorophosphate salt of 2, were structurally characterized. Vitamin-B6 transporting membrane carrier (VTC) mediated entry into tumour cells in preference to the normal ones seems to be responsible for the higher cellular uptake of the complexes into HeLa and MCF-7 cells over MCF-10A cells. Complexes 3 and 4 having acdppz as the photosensitizer exhibit remarkable photocytotoxicity in these cancer cells giving IC50 of < 0.9 mu M. The complexes remain non-toxic in the dark. The complexes show photo-induced apoptotic cell death via singlet oxygen (O-1(2)) generation. Fluorescence microscopy reveals specific localization of complex 4 to endoplasmic reticulum (ER) and generation of O-1(2) possibly leads to apoptotic cell death by triggering ER stress response (ERSR).

Tight triangulations of closed 3-manifolds

A triangulation of a closed 2-manifold is tight with respect to a field of characteristic two if and only if it is neighbourly; and it is tight with respect to a field of odd characteristic if and only if it is neighbourly and orientable. No such characterization of tightness was previously known for higher dimensional manifolds. In this paper, we prove that a triangulation of a closed 3-manifold is tight with respect to a field of odd characteristic if and only if it is neighbourly, orientable and stacked. In consequence, the Kuhnel-Lutz conjecture is valid in dimension three for fields of odd characteristic. Next let F be a field of characteristic two. It is known that, in this case, any neighbourly and stacked triangulation of a closed 3-manifold is F-tight. For closed, triangulated 3-manifolds with at most 71 vertices or with first Betti number at most 188, we show that the converse is true. But the possibility of the existence of an F-tight, non-stacked triangulation on a larger number of vertices remains open. We prove the following upper bound theorem on such triangulations. If an F-tight triangulation of a closed 3-manifold has n vertices and first Betti number beta(1), then (n - 4) (617n - 3861) <= 15444 beta(1). Equality holds here if and only if all the vertex links of the triangulation are connected sums of boundary complexes of icosahedra. (C) 2015 Elsevier Ltd. All rights reserved.

Mitochondrial selectivity and remarkable photocytotoxicity of a ferrocenyl neodymium(III) complex of terpyridine and curcumin in cancer cells

A series of four novel neodymium(III) complexes of the formulation Nd(R-tpy)(O-O)(NO3)(2)] (1-4), where R-tpy is 4'-phenyl-2,2': 6', 2''-terpyridine (Ph-tpy; 1, 2) and 4'-ferrocenyl-2,2': 6', 2''-terpyridine (Fc-tpy; 3, 4); O-O is the conjugate base of acetylacetone (Hacac; 1, 3) or curcumin (Hcurc; 2, 4), are synthesized and characterized. The single crystal structure of 1 shows that the complex is a discrete mononuclear species with the Nd(III) centre in a nine coordinate environment provided by a set of O6N3 donor atoms. Complexes 1 and 3 having the simple acac ligand are prepared as control compounds. Complex 4, possessing an appended ferrocenyl (Fc) and the curcumin moiety, is remarkably photocytotoxic to HeLa and MCF-7 cancer cells in visible light giving respective IC50 values of 0.7 mu M and 2.1 mu M while being significantly less toxic to MCF-10A normal cells (IC50 = 34 mu M) and in the dark (IC50 > 50 mu M). The phenyl appended complex 2, lacking a ferrocenyl moiety, is significantly less toxic to both the cell lines when compared with 4. Complexes 1 and 3, lacking the photoactive curcumin moiety, do not show any apparent toxicity both in light and in the dark. The cell death is apoptotic in nature and is mediated by the light-induced formation of reactive oxygen species (ROS). Fluorescence imaging experiment with HeLa cells reveals mitochondrial accumulation of complex 4 within 4 h of incubation. The complexes bind to calf thymus (ct) DNA with moderate affinity giving K-b values in the range of 10(4)-10(5) M-1. The curcumin complexes 2 and 4 cleave plasmid supercoiled DNA to its nicked circular form in visible light via O-1(2) and (OH)-O-center dot pathways. The presence of the ferrocenyl moiety is likely to be responsible for the enhanced cellular uptake and photocytotoxicity of complex 4. Thus, the mitochondria targeting complex 4, being remarkably cytotoxic in light but non-toxic in the dark and to normal cells, is a potential candidate for photochemotherapeutic applications.