The Callender Lab - Albert Einstein College of Medicine

2019
Computational Studies of Catalytic Loop Dynamics in Yersinia Protein Tyrosine Phosphatase Using Pathway Optimization Methods, H. Deng, S. Ke, R. H. Callender, G. Balakrishnan, T. Spiro, E. May and C. L. Brooks III, J. Phys Chem B 123, 7840-7851 (2019). PMC6752976
General Mathematical Formula for Near Equilibrium Relaxation Kinetics of Basic Enzyme Reactions: Derivation of the Formula and its Applications to Screening for Enzymes Employing Conformational Selection Steps, T. Egawa and R. H. Callender, J. Theoretical Biology 313, 61-70 (2019).
Effect of protein isotope labeling on the catalytic mechanism of lactate dehydrogenase, T. Egawa, H. Deng, E. Chang and R. H. Callender, J Phys Chem B 123, (2019).
2018
Small molecule cores demonstrate non-competitive inhibition of lactate dehydrogenase, B. A. Andrews and R. B. Dyer, Med. Chem. Comm. (2018).
Directed Evolution as a Probe of Rate Promoting Vibrations Introduced via Mutational Change, X. Chen and S. D. Schwartz, Biochemistry (2018). PMC5997552
The Enthalpy-entropy Compensation Phenomenon. Limitations for the Use of Some Basic Thermodynamic Equations, S. Khrapunov, Current Protein and Peptide Science 19, 1088-1091 (2018). PMC6142176
Characterizing the Surface Coverage of Protein–Gold Nanoparticle Bioconjugates, R. Kozlowski, A. Ragupathi and R. B. Dyer, Bioconjugate Chemistry 29, 2691-2700 (2018). PMC6093776
Molecular Dynamics Simulation of the Oil Sequestration Properties of a Nonionic Rhamnolipid, C. M. Luft, E. Munusamy, J. E. Pemberton and S. D. Schwartz, J. Phys. Chem. B. (2018). PMC5931930
Mechanism for Fluorescence Quenching of Tryptophan by Oxamate and Pyruvate: Conjugation and Solvation In-duced Photoinduced Electron Transfer, H.-L. Peng and R. H. Callender, J. Phys. Chem. B 122, 6483-6490 (2018). PMC6038119
Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence, V. L. Schramm and S. D. Schwartz, Biochemsitry 57, 3299-3308 (2018). PMC6008225
2017
Mechanistic insights on human phosphoglucomutase revealed by transition path sampling and molecular dynamics calculations, N. Bras, P. Fernandes, M. Ramos and S. D. Schwartz, Chemistry (2017). PMC5801119
Dual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics, C. M. Davis, M. J. Reddish and R. B. Dyer, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy 178, 185-191 (2017). PMC5346054
Difference FTIR Studies of Substrate Distribution in Triosephosphate Isomerase, H. Deng, J. Vedad, R. Z. B. Desamero and R. H. Callender, J. Phys. Chem B 121, 10036-10045 (2017). PMC5687254
Evolution of Aggregate Structure in Solutions of Anionic Monorhamnolipids: Experimental and Computational Results, R. J. Elsmin, E. Munusamy, L. L. Kegel, D. E. Hogan, R. M. Maier, S. D. Schwartz and J. E. Pemberton, Langmuir 33, 7412-7424. (2017). PMC5767468
Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase, R. Harijan, I. Zoi, D. Antoniou, S. D. Schwartz and V. Schramm, Proc Natl Acad Sci U S A 114, 6456-6461 (2017). PMC5488955
Thermodynamic and structural adaptation differences between mesophilic and psychrophilic lactate dehydrogenases, S. Khrapunov, E. Chang and R. H. Callender, Biochemistry 56, 3587-3595 (2017). PMC5574168
Structural Properties of Nonionic Monorhamnolipid Aggregates in Water Studied by Classical Molecular Dynamics Simulations, E. Munusamy, C. M. Luft, J. E. Pemberton and S. D. Schwartz, J. Phys Chem B 121, 5781-5793 (2017). PMC5562376
Mechanistic Analysis of Fluorescence Quenching of Reduced Nicotinamide Adenine Dinucleotide by Oxamate in Lactate Dehydrogenase Ternary Complexes, H.-L. Peng and R. H. Callender, Photochemistry and Photobiology 93, 1193-1203 (2017). PMC5603363
Resolution of sub-millisecond kinetics of multiple reaction pathways for lactate dehydrogenase , M. Reddish, R. H. Callender and R. B. Dyer, Biophysical J. 112, 1852-1862 (2017). PMC5425397
Structurally Linked Dynamics in Lactate Dehydrogenases of Evolutionarily Distinct Species, M. J. Varga, M. W. Dzierlenga and S. D. Schwartz, Biochemistry 56, 2488-2496 (2017). PMC5507060
Electric Fields and Fast Protein Dynamics in Enzymes., I. Zoi, D. Antoniou and S. D. Schwartz, J. Phys Chem Letters 8, 6165-6170 (2017). PMC5769145
Incorporating Fast Protein Dynamics into Enzyme Design: A Proposed Mutant Aromatic Amine Dehydrogenase, I. Zoi, D. Antoniou and S. D. Schwartz, J. Phys Chem B 121, 7290-7298 (2017). PMC5763476
2016
Phase space bottlenecks in enzymatic reactions, D. Antoniou and S. D. Schwartz, J. Phys. Chem. B 120, 443-439 (2016). PMC4734068
Active Loop Dynamics within the Michaelis complex of lactate dehydrogenase from bsStearothermophilus, N. Beining, K. Lodewyks, H. Deng, R. Desamero and R. H. Callender, Biochemiatry 55, 3803-3814 (2016). PMC5235360
Hydride Transfer in DHFR by Transition Path Sampling, Kinetic Isotope Effects and Heavy Enzyme Studies, Z. Wang, D. Antoniou, S. D. Schwartz and V. Schramm, Biochemistry 55, 157-166 (2016). PMC4752833
Targeting a Rate-Promoting Vibration with an Allosteric Mediator in Lactate Dehydrogenase , M. W. Dzierlenga and S. D. Schwartz, J. Phys. Chem Lett 7, 2591-2596 (2016). PMC4939807
Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models, X. Pan and S. D. Schwartz, J. Phys Chem B 120, 6612-6620 (2016). PMC4945396
Ligand-Dependent Conformational Dynamics of Dihydrofolate Reductase., M. J. Reddish, M. B. Vaughn, R. Fu and R. B. Dyer, Biochemistry 55, 1485-1493 (2016). PMC4806677
Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations, M. J. Varga and S. D. Schwartz, J Chem Theory Comput. 12, 2047-2054 (2016). PMC4829465
Triple Isotope Effects SupportConcerted Hydride andProton Transfer and Promoting Vibrations inHuman Heart Lactate Dehydrogenase, Z. Wang, E. P. Chang and S. V. L., J. Am . Chem. Soc. 138, 15004-15010, (2016). PMC5244818
Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics, I. Zoi, J. Suarez, D. Antoniou, S. A. Cameron, V. L. Schramm and S. D. Schwartz, J. Am . Chem. Soc. 138, 3403-3409 (2016). PMC4794390
Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions, M. W. Dzierlenga, M. J. Varga and S. D. Schwartz, Methods. Enzymol, 578, 21-43 (2016). PMC5026240
2015
The Dynamical Nature of Enzymatic Catalysis, R. Callender and R. B. Dyer, Accounts of Chemical Research 48, 407-413 (2015). PMC4333057
Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling, M. W. Dzierlenga, D. Antoniou and S. D. Schwartz, J. Phys. Chem. Letts. 6, 1177-1181 (2015). PMC4749019
The Pathway of O2 to the Active Site in Heme-Copper Oxidases, O. Einarsdotir, W. McDonald, C. Funatogawa, W. H. Woodrugg and R. B. Dyer, Bioch. Biophs. Acta Bioeneergetiics 1847, 109-118 (2015). PMC4252355
Sandwich-format 3D printed microfluidic mixers: a flexible platform for multi-probe analysis, D. Kise, M. J. Reddish and R. B. Dyer, J. Micromech. Microeng. 25, 124002 (2015). PMC4737954
Evolution alters the enzymatic reaction coordinate of dihydrofolate reductase, J. E. Masterson and S. D. Schwartz, J. Phys. Chem B 119, 989-996 (2015). PMC4306496
Free Energy Surface of the Michaelis Complex of Lactate Dehydrogenase: A Network Analysis of Microsecond Simulations , X. Pan and S. D. Schwartz, J. Phys Chem B 119, 5430-5436 (2015). PMC4748716
Mechanisms of Thermal Adaptation in the Lactate Dehydrogenases, H.-L. Peng, T. Egawa, E. Chang, H. Deng and R. H. Callender, J. Phys. Chem B 119, 15256-15262 (2015). PMC4679558
Isotope-specific and amino acid-specific heavy atom substitutions alter barrier crossing in human purine nucleoside phosphorylase, J. Suarez and V. L. Schramm, Proc Natl Acad Sci U S A 112, 11247-11251 (2015). PMC4568649
Active site and remote contributions to catalysis in methylthioadenosine nucleosidases, K. Thomas, S. A. Cameron, S. C. Almo, E. S. Burgos, S. A. Gulab and V. Schramm, Biochemistry 54, 2520-2529 (2015). PMC4485437
Enzyme homologues have distinct reaction paths through their transition states, I. Zoi, M. Motley, D. Antoniou, V. L. Schramm and S. D. Schwartz, J. Phys. Chem B 119, 3662-3668 (2015). PMC4385586
2014
Submillisecond mixing in a continuous-flow microfluidic mixer utilizing mid-infrared hyperspectral imaging detection, d. P. Kise, D. Magana, M. J. Reddish and R. B. Dyer, Lab Chip 14, 584-591 (2014). PMC3898435
Anisotropic energy flow and allosteric ligand binding in albumin, G. Li, D. Magana and R. B. Dyer, Nature communications 5, 1-7 (2014). PMC3949117
The enzymatic reaction catalyzed by lactate dehydrogenase exhibits one dominant reaction path, J. E. Masterson and S. D. Schwartz, Chemical Physics 442, 132-136 (2014). PMC4215548
The Energy Landscape of the Michaelis Complex of Lactate Dehydrogenase: Relationship to Catalytic Mechanism, H.-L. Peng, H. Deng, R. B. Dyer and R. Callender, Biochemistry 53, 1849-1857 (2014). PMC3985751
Direct Evidence of Catalytic Heterogeneity in Lactate Dehydrogenase by Temperature Jump Infrared Spectroscopy, M. Reddish, H.-L. Peng, H. Deng, K. S. Panwar, R. Callender and R. B. Dyer, J. Phys. Chem B 118, 10854-10862 (2014). PMC4167064
2013
Catalytic Site Conformations in Human PNP by 19F-NMR and Crystallography, J. Suarez, A. M. Haapalainen, S. M. Cahill, M.-C. Ho, F. Yan, S. C. Almo and V. L. Schramm, Chemistry & Biology 20, 212-222 (2013).
Transition States, Analogues, and Drug Development, V. L. Schramm, ACS Chemical Biology 8, 71-81 (2013)
Large Scale Dynamics of the Michaelis Complex of B. Stearothermophilus Lactate Dehydrogenase revealed by Single Tryptophan Mutants Study, B. Nie, H. Deng, R. Desamero and R. Callender, Biochemistry 52, 1886-1892 (2013). pdf
Changes in Protein Architecture and Subpicosecond Protein Dynamics Impact the Reaction Catalyzed by Lactate Dehydrogenase, J. Masterson and S. D. Schwartz, J. Phys. Chem. A 117, 7107-7113 (2013). pdf
Conformational Freedom in Tight Binding Enzymatic Treansition-State Analogues, M. Motley, V. L. Schramm and S. D. Schwartz, J. Phys. Chem B 117, 9591-9597 (2013). PMC3786605
A simple three-dimensional-focusing, continuous-flow mixer for the study of fast protein dynamics, K. S. Burke, D. Parul, M. J. Reddish and R. B. Dyer, Lab Chip 13, 2912-2921 (2013). PMC3733270
2012
A complex of methylthioadenosine/S-adenosylhomocysteine nucleosidase, transition state analogue, and nucleophilic water identified by mass spectrometry, S. Wang, J. Lim, K. Thomas, F. Yan, R. H. Angeletti and V. L. Schramm, J. Am . Chem. Soc. 134, 1468-70 (2012)
Femtomolar Inhibitors Bind to 5'-Methylthioadenosine Nucleosidases with Favorable Enthalpy and Entropy, K. Thomas, Haapalainen, AM, E. S. Bugos, G. B. Evans, P. C. Tyler, S. Gulab, R. Guan and V. L. Schramm, Biochemistry (2012)
Dynamic Differences in Binding Transition State Analogues, M. Motley, V. L. Schramm and S. D. Schwartz, Proc Natl Acad Sci U S A in revision, (2012)
Photo-induced Electron Transfer in Folic Acid Investigated by Ultrrfast Infrared Spectroscopy, G. Li, D. Magana and R. B. Dyer, J. Phys. Chem. B 116, 3467-3475 (2012)
Investigation of Catalytic loop Structure, Dynamics, and Function Relationship of Yersina Protein Tyrosine Phosphatase by Temperature-Jump Relaxation Spectroscopy and X-ray Structural Determination, S. Ke, M.-C. Ho, N. Zhadin, H. Deng and R. Callender, J. Phys. Chem B 116, 6166-6176 (2012)
Direct Observation and Control of Ultrafast Photoinduced Twisted Intramolecular Charge Transfer (TICT) in Triphenyl-Methane Dyes, R. B. Dyer, G. Li and D. Magana, J. Phys. Chem. B 116, 12590-12596 (2012)
Direct evidence of active site reduction and photo-driven catalysis in sensitized hydrogenase assemblies, R. B. Dyer, B. L. Greene, C. A. Joseph and M. J. Maroney, J. Am . Chem. Soc. 134, 11108-11111 (2012)
Barrier Crossing in DHFR Does Not Involve a Rate-Promoting Vibration, M. Dametto, D. Antoniou and S. D. Schwartz, Mol. Phys. 10, 531-536 (2012)
Temperature Dependence of Water Interactions with the Amide Carbonyls of Î±-Helices, S. H. Brewer, S. Gnanakaran, Y. Tang, D. M. Vu, D. P. Raleigh and R. B. Dyer, Biochemistry 51, 5293-2599 (2012)
Mass Modulation of Protein Dynamics Associated with Barrier Crossing in Purine Nucleoside Phosphorylase, D. Antoniou, X. Ge, V. L. Schramm and S. D. Schwartz, J. Phys. Chem Lett 3, 3538-3544 (2012). pdf
2011
The Effect of Osmolytes on Protein Dynamics in the LDH-Catalyzed Reaction, N. Zhadin and R. Callender, Biochemistry 50, 1582-1589 (2011)
Femtosecond Dynamics Coupled to Chemical Barrier Crossing in a Born-Oppenheimer Enzyme, R. G. Silva, A. S. Murkin and V. L. Schramm, Proc. Natl. Acad. Sci. USA 108, 18661-18665 (2011)
Uridine Phosphorylase From Trypanosoma Cruzi: kinetic and chemical mechanism, R. Silva and V. L. Schramm, Biochemistry 42, 9158-9166 (2011)
Arsenate and phosphate as nucleophiles at the transition states of human purine nucleoside phosphorylase, R. Silva, J. S. Hirschi, M. Ghanem, A. S. Murkin and V. L. Schramm, Biochemistry 50, 2701-2709 (2011)
Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes, V. L. Schramm, Ann. Rev. Biochem. 80, 703-732 (2011)
Implementation for a Time-Resolved Step-Scan FTIR Using 1 kHz Repetition Rate pump Laser, D. Magana, D. Parul, R. B. Dyer and A. P. Shreve, Appl. Spect. 65, 535-542 (2011)
Mass-dependent bond vibrational dynamics influence catalysis by HIV-1 protease, D. R. Kipp, R. Silva and V. L. Schramm, J. Am . Chem. Soc. 133, 19358-61 (2011)
Conformational heterogeneity within the Michaelis complex of lactate dehydrogenase, H. Deng, D. V. Vu, K. Clinch, R. Desamero, R. B. Dyer and R. Callender, J, Phys. Chem. B 115, 7670-6778 (2011)
The Promoting Vibration in Human Heart Lactate Dehydrogenase is a Preferred Vibrational Channel, A. Davarifar, D. Antoniou and S. D. Schwartz, J. Phys. Chem B 115, 15439-15444 (2011)
Protein Dynamics and Enzymatic Chemical Barrier Passage, D. Antoniou and S. D. Schwartz, J. Phys. Chem B 115, 15147-15158 (2011)
Towards identification of the reaction coordinate from the transition state ensemble using the kernel PCA method, D. Antoniou and S. D. Schwartz, J. Phys. Chem. B 115, 2465-2469 (2011)
2010
On the Origin of the Chemical Barrier and Tunneling in Enzymes, S. Quaytman-Machleder, E. T. Pineda and S. D. Schwartz, J. Physical Organic Chemistry 23, 690-695 (2010)
Slow Conformational Motions That Favor Sub-picosecond Motions Important for Catalysis, J. R. E. T. Pineda, D. Antoniou and S. D. Schwartz, J. Phys. Chem. B 114, 15985-15990 (2010)
Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues, J. S. Hirschi, K. Arora, C. L. Brooks and V. Schramm, J. Phys. Chem. B 114, 16263-16272 (2010)
Azidohomalanine: A conformationally sensitive IR probe of Protein Folding, Protein Strucutre, and Electrostatics, T.-S. H., J. Chung, P. S. Banerjee, S. Narajan, R. B. Dyer, I. Carrico and D. P. Raleigh, Angew. Chem. IE 49, 7473-7475 (2010)
Conformational States of Human Purine Nucleoside Phosphorylase at Rest, at Work, and with Transition State Analogues, A. A. Edwards, J. D. Tipton, M. D. Brenowitz, M. R. Emmett, A. G. Marshall, G. B. Evans, P. C. Tyler and V. Schramm, Biochemistry 49, 2058-2067 (2010)
Pyrophosphate Activation in Hypoxanthine-Guanine Phosphoribosyltransferase with Transition State Analogue, H. Deng, R. Callender, V. Schramm and C. Grubmeyer, Biochemistry 49, 2705-2714 (2010)
Leaving Group Activation and Pyrophosphate Ionic State at the Catalytic Site of Plasmodium falciparum Orotate Phosphoribosynsferase,Yong Zhang, H. Deng, V. L. Schramm, J. Am. Chem. Soc. 132, 17023-31 (2010). PMC3012390
2009
Enzymatic transition States and Dynamic Motion in Barrier Crossing, S. D. Schwartz and V. Schramm, Nat. Chem. Biol. 5, 551-558 (2009)
Comparison Studies of the Human Heart and Bacillus sterothermophilus Lactate Dehydrogenase by Transition Path Sampling, S. L. Quaytman and S. D. Schwartz, J. Phys. Chem. A 113, 1892-1897 (2009)
Extension of the Tryptophan Dihedral Angle - W3 Band Frequency Relationship to a Full Rotation: Correlations and Caveats, L. J. Juszczak and R. Z. B. Desamero, Biochemistry 48, 2777-2787 (2009)
Loop-Tryptophan Human PNP Reveals Submillisecond Protein Dynamics, M. Ghanem, N. Zhadin, R. Callender and V. Schramm, Biochemistry 48, 3658-3668 (2009)
Ribocation Transition State Capture and Rebound in Human Purine Nucleoside, M. Ghanem, A. S. Murkin and V. Schramm, Chemical Biology 16, 971-979 (2009)
Altered enthalpy-entropy compensation in picomolar transition state analogues of human purine nucleoside phosphorylase, A. A. Edwards, J. M. Mason, K. Clinch, P. C. Tyler, G. B. Evans and V. Schramm, Biochemistry 16, 5226-5238 (2009)
Approximate inclusion of quantum effects in Transition Path Sampling, D. Antoniou and S. D. Schwartz, J. Chem. Phys. 131, 224111 (2009)
The Stochastic Separatrix and Reaction Coordinate for Complex Systems, D. Antoniou and S. D. Schwartz, J. Chem. Physics 130, 151103-151106 (2009)
2008
Probing the Role of Dynamics in Hydride Transfer Catalyzed by Lactate Dehydrogenase, N. Zhadin, M. Gulotta and R. Callender, Biophysical J. 95, 1974-1984 (2008)
TPS Study of the Reaction Catalyzed by Purine Nucleoside Phosphorylase, S. Saen-Oon, V. Schramm and S. D. Schwartz, Z. Physik. Chemie. 222, 1359-1374 (2008)
Atomic Detail of Chemical Transformation at the Transition State of an Enzymatic Detail, S. Saen-Oon, S. Quaytman-Machleder, V. Schramm and S. D. Schwartz, Proc Natl Acad Sci U S A 105, 16543-16548 (2008)
Remote Mutations and Active Site Dynamics Correlate with Catalytic Properties of Purine Nucleoside Phosphorylase, S. Saen-Oon, M. Ghanem, V. Schramm and S. D. Schwartz, Biophysical J. 94, 4078-4088 (2008)
Transition-state interactions revealed in purine nucleoside phosphorylase by binding isotope effects, A. S. Murkin, P. C. Tyler and V. Schramm, J. Am. Chem. Soc. 130, 2166-2167 (2008)
Remote Mutations Alter Transition-State Structure of Human Purine Nucleoside Phosphorylaase, L. Li, M. Luo, M. Ghanem, E. A. Taylor and V. L. Svchramm, Biochemistry 47, 2577-2583 (2008)
Second-Sphere Amino Acids Comtribute to Transition-State Strcuture in Bovine Purine Nucleoside Phosphoralase, L. Li, M. Luo, M. Ghanem, E. A. Taylor and V. Schramm, Biocmeistry 26, 2577-2583 (2008)
Tryptophan-free Human PNP Reveals Catalytic Site Interactions, M. Ghanem, S. Saen-Oon, N. Zhadin, C. Wing, S. Cahill, S. D. Schwartz, R. H. Callender and V. Schramm, Biochemistry 47, 3202-3215 (2008)
Altered Thermodynamics from Remote Mutations Alterning Human toward Bovine Purine Nucleoside Phosphorylase, M. Ghanem, L. Li, C. Wing and V. Schramm, Biocmeistry 26, 2559-2564 (2008)
On the Pathway of Forming Enzymatically Productive Ligand-Protein Complexes in Lactate Dehydrogenase, H. Deng, S. H. Brewer, D. V. Vu, K. Clinch, R. Callender and R. B. Dyer, Biophys. J. 95, 804-813 (2008)
Infrared Evidence for Water Interactions with alpha-Helical proteins, S. H. Brewer, S. Gnanakaran, Y. Tang, D. Vu, D. Raleigh and R. B. Dyer, Biochemistry submitted (2008)
2007
Binding Isotope Effects: boon and bane, V. Schramm, Curr. Opin. Chem. Biol. 11, 529-536 (2007)
Enzymatic Transition State Theory and Transition State Analogue Design, V. Schramm, J. Biol. Chem. 282, 28297-28300 (2007)
Reaction Coordinate of an Enzymic Reaction Revealed by Transition Path Sampling, S. L. Quaytman and S. D. Schwartz, Proc. Natl. Acad. Sci. (USA) 104, 12253-12258 (2007)
Lactate Dehydrogenase Undergoes a Substantial Structural Change to Bind its Substrate, L. Qiu, M. Gulotta and R. Callender, Biophysical J. 93, 1677-1686 (2007)
Ligand Binding and Protein Dynamics in Lactate Dehydrogenase, J. R. E. T. Pineda, R. Callender and S. D. Schwartz, Biophysical J. 93, 1474-1483 (2007)
Neighboring Group participation in the Transition State of Human Purine Nucleoside phosphorylase, A. S. Murkin, M. R. Birck, A. Rinalso-Matthis, W. Shi, E. A. Taylor Ringia and V. Schramm, Biochemistry 46, 5038-5049 (2007)
A Simple and Economical Method for the Production of 13C, 18O-labeled Fmoc-Amino Acids with High Levels of Enrichment: Applications to Isotope-Edited IR Studies of Proteins, J. Marecek, B. Song, S. H. Brewer, J. Belyea, R. B. Dyer and D. Raleigh, Organic Letters 9, 4935-4937 (2007)
Residue Specific Resolution of Protein Folding Dynamics Using Isotope-Edited Infrared Temperature Jump Spectroscopy, S. H. Brewer, B. Song, D. Raleigh and R. B. Dyer, Biochemistry 46, 3279-3285 (2007)
A New Mixed Quantum/Semiclassical Propagation Method, D. Antoniou, D. Gelman and S. D. Schwartz, J. Chem. Phys. 126, 184107-184114 (2007)
2006
Microfluidics flow-flash: Method for Investigating protein Dynamics, M. Toepke, S. H. Brewer, D. V. Vu, K. D. Rector, J. E. Morgan, R. B. Gennis, P. Kenis and R. B. Dyer, Anal. Chem. 79, 122-128 (2006)
Introduction: Principles of Enzymatic Catalysis, V. Schramm, Chem. Rev. 106, 3029-3030 (2006)
Protein Dynamics and Catalysis â€“ The Problems of Transition State Theory and the Subtlety of Dynamic Control, E. T. Pineda and S. D. Schwartz, Phil. Trans. Royal Soc. 361, 1433-1438 (2006)
Temperature and pH dependence of inter-heme electron transfer in bovine cytochrome c oxidase, D. Parul, F. N. Rein, J. A. Bailey, W. H. Woodruff and R. B. Dyer, Biochemistry submitted, (2006)
Insight into Catalytically Relevant Correlated Motions in Human Purine Nucleoside Phosphorylase, S. Nunez, C. Wing, D. Antonoiu, V. Schramm and S. D. Schwartz, J. Phys. Chem. B 110, 463-472 (2006)
Phosphate Activation in the Ground State of Purine Nucleoside Phosphorylase, H. Deng, A. S. Murkin and V. Schramm, J. Am. Chem. Soc. 128, 7765-7771 (2006)
Syntheses and Bio-activities of the L-enantiomers of Two Potent Transition State Analogue Inhibitors of Purine Nucleoside Phosphorylases, K. Clinch, G. B. Evans, G. W. Fleet, R. H. Furneaux, S. W. Johnson, D. H. Lenz, S. P. Mee, P. R. Rands, V. Schramm, E. A. Taylor Ringia and P. C. Tyler, Org. Biomol. Chem. 4, 1131-1139 (2006)
Advances in Time-Resolved Approaches to Characterize the Dynamical Nature of Enzymatic Catalysis, R. H. Callender and R. B. Dyer, Chem. Revs. 106, 3031-3042 (2006)
Time-Resolved Vibrational Spectroscopy detects protein-Based Intermediates in the Photosynthetic Oxygen-evolving Cycle, B. A. Barry, I. B. Cooper, A. DeRiso, S. H. Brewer, D. Vu and R. B. Dyer, Proc. Natl. Acad. Sci. (USA) 103, 7288-7291 (2006)
Computational and Theoretical Methods to Explore the Relationship between Enzyme Dynamics and Catalysis, D. Antoniou, J. E. Basner, S. Nunez and S. D. Schwartz, Chem. Revs. 106, 3170-3187 (2006)
2005
Transition State Aanalgue Discrimination by Related Purine Nucleoside Phosphorylases, E. A. Taylor-Ringia, P. C. Tyler, G. B. Evans, R. H. Furneaux, A. S. Murkin and V. Schramm, J. Am . Chem. Soc. 128, 7126-7127 (2005)
Transition States and Inhibitors of the Purine Nucleoside Phosphorylase Family, E. A. Taylor Ringia and V. Schramm, Curr. Top. Med. Chem. 5, 1237-1258 (2005)
Development of a Tandem Trans-Splicing System based on Native and Engineered Split Inteins, J. Shi and T. W. Muir, J. Am. Chem. Soc. 127, 6198-6206 (2005)
Enzymatic Transition States and Transition State Analogues, V. Schramm, Curr. Opin. Struct. Biol. 15, 604-13 (2005)
Enzymatic Transition States: thermodynamics, dynamics, and analogue design, V. Schramm, Arch. Biochem. Biophys. 433, 13-26 (2005)
The Approach to the Michaelis Complex in Lactate Dehydrogenase: the substrate binding pathway, S. McClendon, N. Zhadin and R. Callender, Biophysical J. 89, 2024-2032 (2005)
Structural Transformations in the Dynamics of Michaelis Complex Formation in Lactate Dehydrogenase, S. McClendon, D. Vu, K. Clinch, R. Callender and R. B. Dyer, Biophysical J. How Enzyme Dynamics Helps Catalyze a Chemical Reaction in Atomic Detail: A Transition Path Sampling Study, J. E. Basner and S. D. Schwartz, J. Am. Chem. Soc. 127, 13822-13831 (2005)
2004
Promoting Motions in Human Purine Nucleoside Phosphorylase: a molecular dynamics and hybrid quantum mechanical/molecular mechanical study, S. Nunez, D. Antoniou, V. Schramm and S. D. Schwartz, J. Am Chem. Soc. 126, 15720-15729 (2004)
Coupling Protein Dynamics to Reaction Center Electron Density in Enzymes: an electronic protein promoting vibration in human purine nucleoside phosphorylase, J. S. Mincer, S. Nunez and S. D. Schwartz, J. of Theoretical and Computational Chemistry 3, 501-510 (2004)
FTIR Studies of Internal Proton Transfer Reactions Linked to Inter-heme Electron Transfer in Bovine Cytochrome c Oxidase, B. H. McMahon, M. Fabian, F. Tomson, T. P. Causgrove, J. A. Bailey, F. N. Rein, R. B. Dyer, G. Palmer, R. B. Gennis and W. H. Woodruff, Bioch. Biophs. Acta 1655, 321-331 (2004)
Activating The Phosphate Nucleophile At The Catalytic Site Of Purine Nucleoside Phosphorylase: a vibrational spectroscopic study, H. Deng, A. Lewandowicz, V. L. Schramm and R. Callender, J. Am. Chem. Soc. 126, 9516-9517 (2004)
Active Site Contacts in the Purine Nucleoside Phosphorylaseâ€¢hypoxanthine Complex by NMR and ab initio Calculations, H. Deng, S. Cahill, A. Lewandowicz, R. Callender, V. Schramm and R. Jones, Biochemistry 43, 15966-15974 (2004)
Donor-Acceptor Distance and Protein Promoting Vibration Coupling to Hydride Transfer: A possible mechanism for kinetic control in isozymes of human lactate dehydrogenase, J. E. Basner and S. D. Schwartz, J. Phys. Chem. B 108, 444-451 (2004)
Transition Path Sampling Study of Classical Rate-Promoting Vibrations, D. Antoniou and S. D. Schwartz, J. Chem. Phys. 121, 6442-6447 (2004)

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