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Journal of Physical Chemistry B, ISSN 1520-6106, 11/2006, Volume 110, Issue 43, pp. 21630 - 21638
Silk fibroin sol-gel transitions were studied by monitoring the process under various physicochemical conditions with optical spectroscopy at 550 nm. The... 
BIOMATERIAL | N-ISOPROPYLACRYLAMIDE | BOMBYX-MORI SILK | TEMPERATURE | CHEMISTRY, PHYSICAL | CONFORMATIONAL TRANSITIONS | VOLUME-PHASE-TRANSITION | INFRARED-SPECTROSCOPY | PROTEINS | POLY(ETHYLENE OXIDE) | Fibroins - chemistry | Molecular Structure | Phase Transition | Hydrogen-Ion Concentration | Proteins | Usage | Spectrum analysis | Gelation | Analysis | Research | Structure
Journal Article
Chemical Physics Letters, ISSN 0009-2614, 06/2018, Volume 702, pp. 82 - 89
The interconversion pathways along the puckering transitions in cyclohexane were explored on the two-dimensional projection of the Cremer-Pople sphere using... 
Puckering transitions | CCSD(T)/CBS-limit energies | DFT calculations | Cyclohexane | Solvent effects | DISPERSION CORRECTIONS | TWIST-BOAT | ENERGY | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | NONCOVALENT INTERACTIONS | SPECTROSCOPY | CHAIR | RING | CONFORMATIONAL-ANALYSIS | DENSITY-FUNCTIONAL THEORY | MAIN-GROUP THERMOCHEMISTRY
Journal Article
Biochimica et biophysica acta. General subjects, ISSN 0304-4165, 04/2019
Human hemoglobin is an allosteric protein that exerts exquisite control over ligand binding through large-scale conformational changes. The two-state model... 
Journal Article
ACS Chemical Biology, ISSN 1554-8929, 01/2013, Volume 8, Issue 1, pp. 71 - 81
Enzymes achieve their transition states by dynamic conformational searches on the femtosecond to picosecond time scale. Mimics of reactants at enzymatic... 
HUMAN THYMIDINE PHOSPHORYLASE | 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE | PURINE NUCLEOSIDE PHOSPHORYLASE | PSEUDOMONAS-AERUGINOSA | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | 5'-METHYLTHIOADENOSINE NUCLEOSIDASE | HIV-1 PROTEASE | ENZYMATIC-REACTION | ADENOSINE DEAMINASE | AMP NUCLEOSIDASE | Enzymes - chemistry | HIV Protease Inhibitors - pharmacology | HIV Protease - drug effects | Models, Biological | Drug Design | Indinavir - pharmacology | Models, Molecular | HIV Protease Inhibitors - chemistry | HIV Protease - chemistry | Kinetics | Indinavir - chemistry | Transition state analysis—the process of measuring intrinsic kinetic isotope effects at sufficient atomic positions to permit reconstruction of a transition state wave function by computational matching of all isotope effects to a quantum chemistry-derived transition state | Dynamic barrier crossing—reactants aligned in the catalytic site by the slow conformational change are subjected to local, fast interactions with catalytic site groups moving on the fsec time scale. When the interactions are optimized by simultaneous chance motion, the barrier to the reaction falls, the transition state is reached and barrier crossing (chemical reaction) can occur | Transition state—the traditional description is a one-dimensional energetic description: the point on the reaction coordinate profile of highest energy relative to substrate | Intrinsic kinetic isotope effects—kinetic isotope effects directly from the chemical step with all obscuring effects removed. Intrinsic kinetic isotope effects report on the bond vibrational status of the labeled reactant atom at the transition state | Transition state analogue—a chemically stable molecule with features of bond lengths, angles and electron density at the van der Waals surface to resemble the actual transition state more closely than it does the reactant. Faithful mimics of enzymatic transition states bind more tightly than substrates by orders of magnitude | Heavy enzyme—enzyme with isotopically substituted atoms to increase the protein mass and thereby decrease the bond vibrational frequency of the protein. Substitution with 2H, 13C and 15N alters mass but not electrostatics according to the Born-Oppenheimer approximation | Transition state structure—a static chemical model of the bond lengths, angles and electron density at the van der Waals surface of the reactant at the instant of the transition state. The transition state structure has a lifetime on the fsec timescale and has equal probability of partitioning to reactant or product | Kinetic isotope effects—the experimentally observed change in reaction rate caused by a specific isotopic substitution in a reactant substrate of the enzyme. Kinetic isotope effects are largest for atoms near the bonds being broken at the transition state but can be partly or fully hidden by kinetic effects obscuring the chemical step | Slow protein conformational changes—enzymes undergo loop, flap and domain motions to bind reactants and release products. These slow conformational changes are necessary steps in an enzymatic catalytic cycle but are too slow to couple to transition state formation
Journal Article
REPORTS ON PROGRESS IN PHYSICS, ISSN 0034-4885, 07/2012, Volume 75, Issue 7, pp. 076601 - 29
Journal Article
Angewandte Chemie International Edition, ISSN 1433-7851, 04/2015, Volume 54, Issue 18, pp. 5378 - 5382
Journal Article
Current Opinion in Structural Biology, ISSN 0959-440X, 2011, Volume 21, Issue 2, pp. 167 - 172
Journal Article
Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, 10/2014, Volume 82, Issue 10, pp. 2831 - 2841
Serine hydroxymethyltransferase (SHMT) is a pyridoxal‐5′‐phosphate (PLP)‐dependent enzyme belonging to the fold type I superfamily, which catalyzes in vivo the... 
psychrophilic enzyme | flexibility | homology modeling | conformational transition | pyridoxal‐5′‐phosphate | X‐ray crystallography | serine hydroxymethyltransferase | holo enzyme | factors | apo enzyme | Apo enzyme | Pyridoxal-5′-phosphate | X-ray crystallography | Serine hydroxymethyltransferase | B' factors | Holo enzyme | Homology modeling | Psychrophilic enzyme | Flexibility | Conformational transition | APO | MECHANISM | RECOGNITION | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | COMPLEXES | pyridoxal-5 '-phosphate | MULTIPLE SEQUENCE ALIGNMENT | PYRIDOXAL 5'-PHOSPHATE | ENZYME | BIOPHYSICS | SECONDARY STRUCTURE | Pyridoxal Phosphate - chemistry | Salmonella typhimurium - growth & development | Bacterial Proteins - chemistry | Crystallography, X-Ray | Pyridoxal Phosphate - metabolism | Coenzymes - metabolism | Glycine Hydroxymethyltransferase - chemistry | Databases, Protein | Apoenzymes - metabolism | Escherichia coli - growth & development | Salmonella typhimurium - enzymology | Coenzymes - chemistry | Recombinant Proteins - metabolism | Glycine Hydroxymethyltransferase - genetics | Catalytic Domain | Gammaproteobacteria - enzymology | Escherichia coli - enzymology | Protein Structure, Secondary | Bacterial Proteins - genetics | Enzyme Stability | Models, Molecular | Recombinant Proteins - chemistry | Escherichia coli Proteins - metabolism | Mutant Proteins - metabolism | Gammaproteobacteria - growth & development | Glycine Hydroxymethyltransferase - metabolism | Protein Folding | Apoenzymes - genetics | Mutant Proteins - chemistry | Apoenzymes - chemistry | Escherichia coli Proteins - genetics | Protein Binding | Bacterial Proteins - metabolism | Protein Conformation | Escherichia coli Proteins - chemistry
Journal Article
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, 05/2017, Volume 178, pp. 142 - 150
A newly designed asymmetrical four-ring bent-core compound (4′- decyloxyphenylazo)-phenyl-4-yl-3-[ -(4′- -octadecyloxy-2-hydroxybenzylidene) amino]-2-methyl... 
TD-FTIR and SmA phase | DSC | PES | POM | TOTAL ENERGIES | INFRARED-SPECTROSCOPY | MOLECULES | DENSITY | MESOMORPHISM | SUBSTITUENT | SPECTROSCOPY | SET MODEL CHEMISTRY | DYNAMICS | CHIRALITY | MICRO-RAMAN | Density functionals | Hydrogen | Analysis | Force and energy | Conformational analysis | Hydrogen bonding
Journal Article