@article { ISI:000241179400014, title = {Hybrid foldamer with unique architecture from conformationally constrained aliphatic-aromatic amino acid conjugate}, journal = {Tetrahedron}, volume = {62}, number = {43}, year = {2006}, month = {OCT}, pages = {10141-10146}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, type = {Article}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

In this paper, we describe the design and synthesis of a novel hybrid foldamer, derived from a conformationally constrained aliphatic-aromatic amino acid conjugate that adopts a well-defined, compact, three-dimensional structure, governed by a combined conformational restriction imposed by the individual amino acids from which the foldamer is composed. Conformational investigations confirmed the prevalence of a unique doubly bent conformation for the foldamer, in both solid and solution states, as evidenced from single crystal X-ray and 2D NOESY studies, respectively. The findings suggest that constrained aliphatic-aromatic amino acid conjugates offer new avenues for the de novo design of hybrid foldamers with distinctive structural architectures. Furthermore, the de novo design strategy disclosed herein has the potential for significantly augmenting the {\textquoteleft}tool-box{\textquoteright} of the modern day peptidominetic chemist, as well as providing a novel approach to the field of rational design. (c) 2006 Elsevier Ltd. All rights reserved.

}, keywords = {Amino acids, Conformation, Foldamer, Peptidomimetics}, issn = {0040-4020}, doi = {10.1016/j.tet.2006.08.032}, author = {Srinivas, Deekonda and Gonnade, Rajesh G. and Ravindranathan, Sapna and Sanjayan, Gangadhar J.} } @article { ISI:000245369300017, title = {Correlation between mobility enhancement and conformational change in polyaniline and its derivatives: polaron lattice formation}, journal = {Electrochimica Acta}, volume = {52}, number = {11}, year = {2007}, month = {MAR}, pages = {3615-3620}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, type = {Article}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

Conformational changes in polyaniline, poly(methyl aniline), and poly(methoxyaniline) are studied in perchloric acid and acetonitrile by means of an in situ reflection technique with oxidation level as a parameter. Stretching of polymer chains leading to enhancement of specular reflection at the polymer-coated electrodes is found to be well correlated with the increase in carrier mobility. The concomitant change in mobility and chain conformation observed with the polyaniline family is explained in terms of the formation of polaron lattice at increased oxidation levels. (c) 2006 Elsevier Ltd. All rights reserved.

}, keywords = {Conformation, polyaniline, reflection, scattering : mobility}, issn = {0013-4686}, doi = {10.1016/j.electacta.2006.10.040}, author = {Harima, Yutaka and Ogawa, Fumiyuki and Patil, Rahul and Jiang, Xiaoqing} } @article { ISI:000246869200003, title = {New technique to study kinetics of chain conformation in polyaniline films}, journal = {Polymer Journal}, volume = {39}, number = {4}, year = {2007}, month = {FEB}, pages = {296-297}, publisher = {SOC POLYMER SCIENCE JAPAN}, type = {Article}, address = {TSUKIJI DAISAN NAGAOKA BLDG, 2-4-2 TSUKIJI, CHUO-KU, TOKYO, 104, JAPAN}, keywords = {Conformation, kinetics, laser, polyaniline, reflection}, issn = {0032-3896}, doi = {10.1295/polymj.PJ2006188}, author = {Harima, Yutaka and Kishimoto, Kazuya and Ogawa, Fumiyuki and Jiang, Xiaoqing and Patil, Rahul} } @article { ISI:000281980600018, title = {Conformational polymorphism in racemic 2,4-Di-o-Benzoyl-6-o-Tosyl myo-Inositol 1,3,5-Orthoacetate}, journal = {Journal of Structural Chemistry}, volume = {51}, number = {4}, year = {2010}, month = {AUG}, pages = {725-730}, publisher = {SPRINGER}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

The title compound, C(29)H(26)O(10)S, yields two conformational polymorphs concomitantly from dichloromethane-methanol mixture; the major polymorph grows as plates (Form I, monoclinic, P2(1)/n) and the minor polymorph grows as needles (Form II, triclinic, P-1). The two forms differ mainly in orientation of the tosyl group. In Form I, sulfonyl oxygen of the tosyl group makes intermolecular C -HaEuro broken vertical bar O interactions, whereas the same group in Form II is involved in an intramolecular short dipolar S=OaEuro broken vertical bar C=O (sulfonyl-carbonyl) contact. The molecular organization and the influence of various weak non-covalent interactions that stabilize these conformers in the crystal lattices are discussed.

}, keywords = {Conformation, crystal structure, dipolar interactions, Inositol, non-covalent interactions, polymorphism, sulfonyl-carbonyl contact}, issn = {0022-4766}, doi = {10.1007/s10947-010-0107-y}, author = {Manoj, Kochunnoonny and Gonnade, Rajesh G. and Bhadbhade, Mohan M. and Shashidhar, M. S.} } @article { ISI:000288979400008, title = {Facile synthesis of N-benzylated 3-alkyl-2,6-diarylpiperidin-4-ones: Stereochemical investigation by 1D/2D NMR and single-crystal XRD}, journal = {Journal of Molecular Structure}, volume = {990}, number = {1-3}, year = {2011}, month = {MAR}, pages = {44-56}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

A series of thirteen 1-benzyl-3-alkyl-2,6-diarylpiperidin-4-ones 14-26 were conveniently synthesized in high yields 87-92\%. In order to find the impact on piperidone stereochemistry, beside the N-benzylation, methyl/ethyl/isopropyl groups at C-3 and halo/alkyl/alkoxy/benzyloxy groups on the phenyl rings at C-2/C-6 were introduced. All the synthesized compounds were characterized by mass, (1)H and (13)C NMR spectral studies. Of them, the 1-benzyl-3-ethyl-2,6-diphenylpiperidin-4-one 22 was completely characterized by 2D NMR techniques such as (1)H-(1)H COSY, (1)H-(13)C COSY and NOESY to assign the signals, unambiguously. The proton coupling constants and NOE correlations provided the complete stereochemistry of 22, which is further witnessed by its single-crystal XRD analysis. The NMR and XRD studies revealed that the compound 22 exists in a chair conformation with equatorial orientation of all the substituents in both solution and solid states. On the basis of their vicinal coupling constants, the chair conformation with equatorial orientation of the substituents at C-2, C-3, C-6 and N is proposed for all compounds 14-26; moreover, a considerable population of boat conformation also suggested for the compound 26 along with the predominant chair conformation, in solution. (C) 2011 Elsevier B.V. All rights reserved.

}, keywords = {2D NMR, Conformation, N-benzylation, Piperidin-4-one, single-crystal XRD, Stereochemistry}, issn = {0022-2860}, doi = {10.1016/j.molstruc.2010.12.054}, author = {Dindulkar, Someshwar D. and Parthiban, Paramasivam and Puranik, Vedavati G. and Jeong, Yeon Tae} } @article { ISI:000308300700010, title = {Prediction of structure and energy of trans-1,4-polybutadiene glassy surface by atomistic simulations of free-standing ultrathin films}, journal = {Journal of Macromolecular Science Part B-Physics}, volume = {51}, number = {11}, year = {2012}, month = {MAR}, pages = {2201-2221}, publisher = {TAYLOR \& FRANCIS INC}, type = {Article}, address = {325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA}, abstract = {

Atomistic modeling of amorphous trans-1,4-polybutadiene (TPBD), using molecular mechanics and molecular dynamics (MD) simulations, is performed to generate three-dimensionally periodic bulk and two-dimensionally periodic thin film condensed phases. The condensed structures are constructed using multiple polymer chains. Structural and energetic relaxations and sampling of properties are performed using MD in the canonical ensemble (NVT) by a procedure that relieves local high-energy spots and brings the system to realistic thermodynamic states. The calculated surface energy for TPBD, 30.72 erg/cm(2), is in excellent agreement with the reported experimental value of 31 erg/cm(2). The structure of the surface layers is probed in terms of the atomic mass density variations, bond-bond orientation function profiles, and the distribution of the dihedral angles about the rotatable backbone bonds. The thickness of the surface layer over which the density varies smoothly but rapidly is found to be approximately 15 angstrom. The level of agreement of the calculated surface energy with the experimental value is superior in comparison to previous investigations in the literature using the atomistic approach for flexible polymers.

}, keywords = {4-polybutadiene, atomistic simulation, bond-orientation, Conformation, molecular dynamics, polymer glass, surface energy, trans-1}, issn = {0022-2348}, doi = {10.1080/00222348.2012.669683}, author = {Ijantkar, Ashwini S. and Natarajan, Upendra} } @article { ISI:000315370000010, title = {Polyproline fold-In imparting kinetic stability to an alkaline serine endopeptidase}, journal = {Biochimica Et Biophysica Acta-Proteins and Proteomics}, volume = {1834}, number = {3}, year = {2013}, month = {MAR}, pages = {708-716}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

Polyproline II (PPII) fold, an unusual structural element was detected in the serine protease from Nocardiopsis sp. NCIM 5124 (NprotI) based on far UV circular dichroism spectrum, structural transitions of the enzyme in presence of GdnHCl and a distinct isodichroic point in chemical and thermal denaturation. The functional activity and conformational transitions of the enzyme were studied under various denaturing conditions. Enzymatic activity of NprotI was stable in the vicinity of GdnHCl upto 6.0 M concentration, organic solvents viz, methanol, ethanol, propanol (all 90\% v/v), acetonitrile (75\% v/v) and proteases such as trypsin, chymottypsin and proteinase K (NprotI:protease 10:1). NprotI seems to be a kinetically stable protease with a high energy barrier between folded and unfolded states. Also, an enhancement in the activity of the enzyme was observed in 1 M GdnHCl upto 8 h, in organic solvents (75\% v/v) for 72 h and in presence of proteolytic enzymes. The polyproline fold remained unaltered or became more prominent under the above mentioned conditions. However, it diminished gradually during thermal denaturation above 60 degrees C. Thermal transition studies by differential scanning calorimetry (DSC) showed scan rate dependence as well as irreversibility of denaturation, the properties characteristic of kinetically stable proteins. This is the first report of PPII helix being the global conformation of a non structural protein, an alkaline serine protease, from a microbial source, imparting kinetic stability to the protein. (C) 2013 Elsevier B.V. All rights reserved.

}, keywords = {Conformation, differential scanning calorimetry, Kinetic stability, Nocardiopsis sp., Polyproline fold, Serine protease}, issn = {1570-9639}, doi = {10.1016/j.bbapap.2012.12.007}, author = {Rohamare, Sonali B. and Dixit, Vaishali and Nareddy, Pavan Kumar and Sivaramakrishna, D. and Swamy, Musti J. and Gaikwad, Sushama M.} } @article { ISI:000334147300006, title = {Conformational transitions of cinnamoyl CoA reductase 1 from leucaena leucocephala}, journal = {International Journal of Biological Macromolecules }, volume = {64}, year = {2014}, month = {MAR}, pages = {30-35}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

Conformational transitions of cinnamoyl CoA reductase, a key regulatory enzyme in lignin biosynthesis, from Leucaena leucocephala (L1-CCRH1) were studied using fluorescence and circular dichroism spectroscopy. The native protein possesses four trp residues exposed on the surface and 66\% of helical structure, undergoes rapid structural transitions at and above 45 C and starts forming aggregates at 55 C. LI-CCRH1 was transformed into acid induced (pH 2.0) molten globule like structure, exhibiting altered secondary structure, diminished tertiary structure and exposed hydrophobic residues. The molten globule like structure was examined for the thermal and chemical stability. The altered secondary structure of Ll -CCRH1 at pH 2.0 was stable up to 90 C. Also, in presence of 0.25 M guanidine hydrochloride (GdnHCI), it got transformed into different structure which was stable in the vicinity of 2 M GdnHCI (as compared to drastic loss of native structure in 2 M GdnHC1) as seen in far UV-CD spectra. The structural transition of LI-CCRH1 at pH 2.0 followed another transition after readjusting the pH to 8.0, forming a structure with hardly any similarity to that of native protein. (C) 2013 Elsevier B.V. All rights reserved.

}, keywords = {Aggregation Cinnamoyl CoA reductase, Conformation, Molten globule, Thermostability, Unfolding}, issn = {0141-8130}, doi = {10.1016/j.ijbiomac.2013.11.024}, author = {Sonawane, Prashant D. and Khan, Bashir Mohammad and Gaikwad, Sushama M.} } @article { ISI:000364613700010, title = {Construction and structural diversity of Cd-MOFs with pyrazole based flexible ligands and positional isomer of naphthalenedisulfonate}, journal = {Inorganic Chemistry Communications}, volume = {61}, year = {2015}, month = {NOV}, pages = {35-40}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

In the present communication, we have reported the construction of a series of Cd(II)-MOFs using conformationally flexible ligand (CFL); 3,3{\textquoteright},5,5{\textquoteright}-tetramethy1-4,4{\textquoteright}-bipyrazolyl (H(2)BPz), flexible bent ligand (FBL); methylenebis-(3,5-dimethylpyrazole) (H(2)MBPz) and positional isomer of naphthalene disulfonic acid salt ligands (1,5-NDS, 2,6-NDS). By using these ligands, four new coordination polymers namely [Cd(H(2)MBPz)(2) center dot 1,5-NDSA](n) (NDS-MOF-1), [Cd(H(2)BPz)center dot 1,5-NDSA](n) (NDS-MOF-2), {[Cd(H(2)MBPz)(2)](2+)center dot 2,6-NDSA(2-)}(n), (NDS-MOF-3) and {[Cd(H(2)BPz)(2)](2+).2,6-NDSA(n)(2-}) (NDS-MOF-4) have been synthesized. The crystal structure analysis revealed that the employment of positional isomeric naphthalene disulfonic acid salts resulted in different architectures ranging from one dimensional chain to two dimensional grid network and further connected into a three dimensional supramolecular structure through intermolecular hydrogen bonds, pi center dot center dot center dot pi and C-H center dot center dot center dot pi interactions. In addition, the photophysical properties and thermal stability studies for all the NDS-M0F5 1-4 were also investigated. (C) 2015 Elsevier B.V. All rights reserved.

}, keywords = {Cadmium(II), Conformation, coordination polymers, Naphthalenedisulfonate, Photophysical properties, thermal stability}, issn = {1387-7003}, doi = {10.1016/j.inoche.2015.08.009}, author = {Singh, Udai P. and Singh, Neetu and Chandra, Suman} } @article {45551, title = {Investigation of structural and saccharide binding transitions of Bauhinia purpurea and Wisteria floribunda lectins}, journal = {Archives of Biochemistry and Biophysics}, volume = {662}, year = {2019}, month = {FEB }, pages = {134-142}, type = {Article}, abstract = {

Two novel medicinally important legume lectins from Bauhinia purpurea (BPL) and Wisteria floribunda (WFL) possessing extended sugar binding site were investigated for functional and conformational transitions using biochemical and biophysical techniques as well as bioinformatical tools. Homology model of BPL was constructed using the Schrodinger suite and docked with N-acetyl galactosamine and T-antigen disaccharide (Gal beta 1-3GalNAc alpha O-Me). The longer loop D in the structure of WFL compared to that in BPL was found to be responsible for its specificity to LacdiNac (beta-D-GalNAc-[1 -\> 4]-DGlcNAc) over Gal beta 1-3GalNAc. BPL remained functionally stable up to 40 degrees C whereas WFL remained stable upto 70 degrees C indicating the strength of the sugar binding site geometry. Both the lectins showed intense but non-specific secondary structure in the range of 65-90 degrees C. WFL showed rapid aggregation above 80 degrees C as indicated by light scattering intensity. The lectins showed simultaneous dissociation and multistate unfolding in the vicinity of GdnHCl. At pH 1.0, both the lectins exhibited molten globule like structures, which were characterized further and were found to respond in a different way towards denaturants. The results have provided valuable insights into the molecular basis of the activity and stability of the two lectins.

}, keywords = {Conformation, Homology model, Lectin, Molten globule, saccharide binding, Thermal aggregation}, issn = {0003-9861}, doi = {10.1016/j.abb.2018.12.003}, author = {Agrawal, Sanskruthi B. and Ghosh, Deepanjan and Gaikwad, Sushama M.} }