Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics

The hydrophobic effect is widely believed to be an important determinant of protein stability. However, it is difficult to obtain unambiguous experimental estimates of the contribution of the hydrophobic driving force to the overall free energy of folding. Thermodynamic and structural studies of large to small substitutions in proteins are the most direct method of measuring this contribution. We have substituted the buried residue Phe8 in RNase S with alanine, methionine, and norleucine, Binding thermodynamics and structures were characterized by titration calorimetry and crystallography, respectively. The crystal structures of the RNase S F8A, F8M, and F8Nle mutants indicate that the protein tolerates the changes without any main chain adjustments, The correlation of structural and thermodynamic parameters associated with large to small substitutions was analyzed for nine mutants of RNase S as well as 32 additional cavity-containing mutants of T4 lysozyme, human lysozyme, and barnase. Such substitutions were typically found to result in negligible changes in Delta C-p and positive values of both Delta Delta H degrees and aas of folding. Enthalpic effects were dominant, and the sign of Delta Delta S is the opposite of that expected from the hydrophobic effect. Values of Delta Delta G degrees and Delta Delta H degrees correlated better with changes in packing parameters such as residue depth or occluded surface than with the change in accessible surface area upon folding. These results suggest that the loss of packing interactions rather than the hydrophobic effect is a dominant contributor to the observed energetics for large to small substitutions. Hence, estimates of the magnitude of the hydrophobic driving force derived from earlier mutational studies are likely to be significantly in excess of the actual value.

Open manifolds, Ozsvath-Szabo invariants and exotic R-4 ` S

We construct an invariant of certain open four-manifolds using the Heegaard Floer theory of Ozsvath and Szabo. We show that there is a manifold X homeomorphic to R-4 for which the invariant is non-trivial,showing that X is an exotic R-4. This is the first invariant that detects exotic R-4' s. (C) 2009 Published by Elsevier GmbH.

An enantiospecific approach to thapsanes from R-carvone: synthesis of (−)-thaps-8-en-5-ol†

The first enantiospecific synthesis of a thapsane, containing three contiguous quaternary carbon atoms, is accomplished starting from R-carvone. An intramolecular alkylation and an intramolecular diazoketone cyclopropanation reaction were employed for the stereo- and regiospecific generation of three contiguous quaternary carbon atoms present in the thapsane framework.

A new chiral oxazoline derived from camphor and its conversion to (R)-2-methylalkanoic acids

1S,5R,7R)-(-)-10, 10-Dimethyl-3-ethyl-4-oxa--atricyclo[5.2.1.0(1,5)]dec-2-ene 2 was prepared in 95% yield from (1S)-1-amino-2-exo-hydroxyapocamphane 1. The chiral oxazoline could be alkylated (Lhttp://eprints.iisc.ernet.in/cgi/users/home?screen=EPrint::Edit&eprintid=31175&stage=core#tDA/THF/-78 degrees C/RX, RX = ethyl, n-propyl, n-butyl iodides or benzyl bromide) to 3 in 95% yield and > 95% diastereoselectivity, and the products hydrolysed to (R)-2-methylalkanoic acids 4 (43-47% yield, 93-98% e.e.). (C) 2000 Elsevier Science Ltd. All rights reserved.

Chiral synthons from carvone, Part 40. A simple, enantiospecific approach to both enantiomers of 1 alpha,25-dihydroxyvitamin D-3 A-ring precursors from R-carvone

A simple and direct approach to both enantiomeric series of A-ring derivatives of 1 alpha,25-dihydroxyvitamin D-3 and the corresponding 1 alpha,3 alpha-derivatives, starting from the abundantly available R-carvone, is described. (C) 2000 Elsevier Science Ltd. All rights reserved.

An enantiospecific approach to pinguisanes from (R)-carvone. Total synthesis of (+)-pinguisenol

Enantiospecific total synthesis of (+)-pinguisenol 1, a sesquiterpene containing a cis-1,2,6,7-tetramethylbicyclo[4.3.0]nonane carbon framework incorporating two vicinal quaternary carbon atoms and four cis-oriented methyl groups on four contiguous carbon atoms, isolated from a liverwort, is described. The orthoester Claisen rearrangement of the allyl alcohol 9, obtained from (R)-carvone, generates the ester 12. Intramolecular cyclopropanation of the diazo ketone 13, derived from the ester 12, furnishes the tricyclic ketone 7. Degradation of the isopropenyl group followed by regioselective reductive cyclopropane ring cleavage transforms compound 7 into the hydroxy ketone 21. Wolff–Kishner reduction of the hydroxy ketone 21 followed by oxidation and Grignard reaction furnishes pinguisenol (+)- 1.

Metabolism of a monoterpene ketone, R-(+)-pulegone—a hepatotoxin in rat

R-(+)-Pulegone was administered orally to rats and the urinary metabolites were investigated. Six metabolites were isolated and purified using column and thin layer chromatographic techniques. Metabolites were identified by i.r., n.m.r. and mass spectral analyses.The neutral metabolites isolated from urine of rats treated with pulegone (I) were: pulegol (II), 2-hydroxy-2(1'-hydroxy-1'-methylethyl)-5-methylcyclohexanone (III), 3,6-dimethyl-7a-hydroxy-5,6,7,7a-tetrahydro-2(4H)-benzofuranone (V) and menthofuran (VII). Metabolites II and III were also excreted in conjugated form.Acidic metabolites isolated from urine of rats treated with pulegone (I) were: 5-methyl-2(1'-methyl-1'-carboxyethylidene)cyclohexanone (IV) and 5-methyl-5-hydroxy-2(1'hydroxy-'-carboxyethyl)cyclohexanone (VI).

Crystal structure and conformation study of N-methyl-t-3-methyl-r-2, c-6-diphenylpiperidin-4-one thiosemicarbazone

Thiosemicarbazones are having the ability to bind with metal and inhibit the enzyme ribonucleoside diphosphate reductase(RDR),an enzyme which is involved in the synthesis of DNA precursors in the mammalian cells.The title compound N-methyl-t-3-methyl-r-2, c-6-diphenylpiperidin-4-one thiosemicarbazone (NMMDPT), CCDC 218052, was prepared using Mannich reaction and characterized by X-ray diffraction methods.The crystal data are:C20H24N4S; M.W= 352.49, triclinic,space group P (1) over bar, a = 8.467(2)angstrom, b = 10.228(2)angstrom, c = 12.249(2)angstrom; lpha=92.595(3)degrees, beta=104.173(3)degrees, gamma=13.628(3)degrees; V=930.0(3)angstrom(3), Z=2, D-cal=1.259Mgm(-3),mu=0.184mm(-1),lambda (MoKalpha)=0.71073 angstrom, final R1 and wR2 are 0.0470 and 0.1052, respectively. The piperidine rings adopt chair conformation. The planar phenyl rings are oriented equatorially at 2,6-positions of the piperidine ring. The molecular packing can be viewed as dimers held together by two N-H...S types of intermolecular hydrogen bonds. Weak C-H...pi interactions also support the stability of the molecules in the crystal in addition to van der Waals forces. (c) 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

13C-N.M.R. studies of discotics

13C-N.M.R. spectra of benzene-hexa-n-octanoate (a discotic liquid-crystalline material) show significant differences in the isotropic, mesomorphic and solid states. The presence of four molecules per asymmetric unit is required to explain the results in the solid state.

Support theorems on R-n and non-compact symmetric spaces

We consider convolution equations of the type f * T = g, where f, g is an element of L-P (R-n) and T is a compactly supported distribution. Under natural assumptions on the zero set of the Fourier transform of T, we show that f is compactly supported, provided g is. Similar results are proved for non-compact symmetric spaces as well. (C) 2010 Elsevier Inc. All rights reserved.

Molecular conformation of alamethicin in dimethylsulfoxide solution A two-dimensional n.m.r. study

The solution conformation of alamethicin, a 20-residue antibiotic peptide, has been investigated using two-dimensional n.m.r. spectroscopy. Complete proton resonance assignments of this peptide have been carried out using COSY, SUPERCOSY, RELAY COSY and NOESY two-dimensional spectroscopies. Observation of a large number of nuclear Overhauser effects between sequential backbone amide protons, between backbone amide protons and CβH protons of preceding residues and extensive intramolecular hydrogen bonding patterns of NH protons has established that this polypeptide is in a largely helical conformation. This result is in conformity with earlier reported solid state X-ray results and a recent n.m.r. study in methanol solution (Esposito et al. (1987) Biochemistry26, 1043-1050) but is at variance with an earlier study which favored an extended conformation for the C-terminal half of alamethicin (Bannerjee et al.

Studies on active site mutants of P-falciparum adenylosuccinate synthetase: Insights into enzyme catalysis and activation

Adenylosuccinate synthetase catalyzes a reversible reaction utilizing IMP, GTP and aspartate in the presence of Mg2+ to form adenylosuccinate, GDP and inorganic phosphate. Comparison of similarly liganded complexes of Plasmodium falciparum, mouse and Escherichia coil AdSS reveals H-bonding interactions involving nonconserved catalytic loop residues (Asn429, Lys62 and Thr307) that are unique to the parasite enzyme. Site-directed mutagenesis has been used to examine the role of these interactions in catalysis and structural organization of P. falciparum adenylosuccinate synthetase (PfAdSS). Mutation of Asn429 to Val, Lys62 to Leu and Thr307 to Val resulted in an increase in K-m values for IMP, GTP and aspartate, respectively along with a 5 fold drop in the k(cat) value for N429V mutant suggesting the role of these residues in ligand binding and/or catalysis. We have earlier shown that the glycolytic intermediate, fructose 1,6 bisphosphate, which is an inhibitor of mammalian AdSS is an activator of the parasite enzyme. Enzyme kinetics along with molecular docking suggests a mechanism for activation wherein F16BP seems to be binding to the Asp loop and inducing a conformation that facilitates aspartate binding to the enzyme active site. Like in other AdSS, a conserved arginine residue (Arg155) is involved in dimer crosstalk and interacts with IMP in the active site of the symmetry related subunit of PfAdSS. We also report on the iochemical characterization of the arginine mutants (R155L, R155K and R155A) which suggests that unlike in E. coil AdSS, Arg155 in PfAdSS influences both ligand binding and catalysis. (C) 2010 Elsevier B.V. All rights reserved.

Generation of a Manganese Specific Restriction Endonuclease with Nicking Activity

A typical feature of type II restriction endonucleases (REases) is their obligate sequence specificity and requirement for Mg2+ during catalysis. R.KpnI is an exception. Unlike most other type II REases, the active site of this enzyme can accommodate Mg2+, Mn2+, Ca2+, or Zn2+ and cleave DNA. The enzyme belongs to the HNH superfamily of nucleases and is characterized by the presence of a beta beta alpha-Me finger motif. Residues D148, H149, and Q175 together form the HNH active site and are essential for Mg2+ binding and catalysis. The unique ability of the enzyme to cleave DNA in the presence of different metal ions is exploited to generate mutants that are specific to one particular metal ion. We describe the generation of a Mn2+-dependent sequence specific endonuclease, defective in DNA cleavage with Mg2+ and other divalent metal ions. In the engineered mutant, only Mn2+ is selectively bound at the active site, imparting Mn2+-mediated cleavage. The mutant is impaired in concerted double-stranded DNA cleavage, leading to accumulation of nicked intermediates. The nicking activity of the mutant enzyme is further enhanced by altered reaction conditions. The active site fluidity of R Eases allowing flexible accommodation of catalytic cofactors thus forms a basis for engineering selective metal ion-dependent REase additionally possessing nicking activity.