Das D.,Massachusetts Institute of Technology |
Kuzmic P.,BioKin Ltd. |
Imperiali B.,Massachusetts Institute of Technology
Proceedings of the National Academy of Sciences of the United States of America | Year: 2017
Phosphoglycosyl transferases (PGTs) are integralmembrane proteins with diverse architectures that catalyze the formation of polyprenol diphosphate-linked glycans via phosphosugar transfer from a nucleotide diphosphate-sugar to a polyprenol phosphate. There are two PGT superfamilies that differ significantly in overall structure and topology. The polytopic PGT superfamily, represented by MraY and WecA, has been the subject of many studies because of its roles in peptidoglycan and O-antigen biosynthesis. In contrast, less is known about a second, extensive superfamily of PGTs that reveals a core structure with dual domain architecture featuring a C-terminal soluble globular domain and a predicted N-terminal membraneassociated domain. Representative members of this superfamily are the Campylobacter PglCs, which initiate N-linked glycoprotein biosynthesis and are implicated in virulence and pathogenicity. Despite the prevalence of dual domain PGTs, their mechanism of action is unknown. Here, we present the mechanistic analysis of PglC, a prototypic dual domain PGT from Campylobacter concisus. Using a luminescence-based assay, together with substrate labeling and kinetics-based approaches, complementary experiments were carried out that support a ping-pong mechanism involving a covalent phosphosugar intermediate for PglC. Significantly, mass spectrometrybased approaches identified Asp93, which is part of a highly conserved AspGlu dyad found in all dual domain PGTs, as the active-site nucleophile of the enzyme involved in the formation of the covalent adduct. The existence of a covalent phosphosugar intermediate provides strong support for a ping-pong mechanism of PglC, differing fundamentally from the ternary complex mechanisms of representative polytopic PGTs.
Johnson C.W.,Northeastern University |
Reid D.,Northeastern University |
Parker J.A.,Northeastern University |
Salter S.,Northeastern University |
And 3 more authors.
Journal of Biological Chemistry | Year: 2017
H-Ras, K-Ras, and N-Ras are small GTPases that are important in the control of cell proliferation, differentiation, and survival, and their mutants occur frequently in human cancers. The G-domain, which catalyzes GTP hydrolysis and mediates downstream signaling, is 95% conserved between the Ras isoforms. Because of their very high sequence identity, biochemical studies done on H-Ras have been considered representative of all three Ras proteins. We show here that this is not a valid assumption. Using enzyme kinetic assays under identical conditions, we observed clear differences between the three isoforms in intrinsic catalysis of GTP by Ras in the absence and presence of the Ras-binding domain (RBD) of the c-Raf kinase protein (Raf-RBD). Given their identical active sites, isoform G-domain differences must be allosteric in origin, due to remote isoform-specific residues that affect conformational states. We present the crystal structure of N-Ras bound to a GTP analogue and interpret the kinetic data in terms of structural features specific for H-, K-, and N-Ras. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
Salykin A.,Masaryk University |
Salykin A.,St Annes University Hospital Brno |
Kuzmic P.,BioKin Ltd |
Kyrylenko O.,Masaryk University |
And 6 more authors.
Stem Cell Reviews and Reports | Year: 2013
Recent evidence suggests that energy metabolism contributes to molecular mechanisms controlling stem cell identity. For example, human embryonic stem cells (hESCs) receive their metabolic energy mostly via glycolysis rather than mitochondrial oxidative phosphorylation. This suggests a connection of metabolic homeostasis to stemness. Nicotinamide adenine dinucleotide (NAD) is an important cellular redox carrier and a cofactor for various metabolic pathways, including glycolysis. Therefore, accurate determination of NAD cellular levels and dynamics is of growing importance for understanding the physiology of stem cells. Conventional analytic methods for the determination of metabolite levels rely on linear calibration curves. However, in actual practice many two-enzyme cycling assays, such as the assay systems used in this work, display prominently nonlinear behavior. Here we present a diaphorase/ lactate dehydrogenase NAD cycling assay optimized for hESCs, together with a mechanism-based, nonlinear regression models for the determination of NAD+, NADH, and total NAD. We also present experimental data on metabolic homeostasis of hESC under various physiological conditions. We show that NAD+/NADH ratio varies considerably with time in culture after routine change of medium, while the total NAD content undergoes relatively minor changes. In addition, we show that the NAD+/NADH ratio, as well as the total NAD levels, vary between stem cells and their differentiated counterparts. Importantly, the NAD+/NADH ratio was found to be substantially higher in hESC-derived fibroblasts versus hESCs. Overall, our nonlinear mathematical model is applicable to other enzymatic amplification systems. © 2013 Springer Science+Business Media New York.
Kleckner I.R.,Ohio State University |
McElroy C.A.,Ohio State University |
Kuzmic P.,BioKin Ltd. |
Gollnick P.,State University of New York at Buffalo |
Foster M.P.,Ohio State University
Biochemistry | Year: 2013
The trp RNA-binding attenuation protein (TRAP) assembles into an 11-fold symmetric ring that regulates transcription and translation of trp-mRNA in bacilli via heterotropic allosteric activation by the amino acid tryptophan (Trp). Whereas nuclear magnetic resonance studies have revealed that Trp-induced activation coincides with both microsecond to millisecond rigidification and local structural changes in TRAP, the pathway of binding of the 11 Trp ligands to the TRAP ring remains unclear. Moreover, because each of 11 bound Trp molecules is completely surrounded by protein, its release requires flexibility of Trp-bound (holo) TRAP. Here, we used stopped-flow fluorescence to study the kinetics of Trp binding by Bacillus stearothermophilus TRAP over a range of temperatures and observed well-separated kinetic steps. These data were analyzed using nonlinear least-squares fitting of several two- and three-step models. We found that a model with two binding steps best describes the data, although the structural equivalence of the binding sites in TRAP implies a fundamental change in the time-dependent structure of the TRAP rings upon Trp binding. Application of the two-binding step model reveals that Trp binding is much slower than the diffusion limit, suggesting a gating mechanism that depends on the dynamics of apo TRAP. These data also reveal that dissociation of Trp from the second binding mode is much slower than after the first Trp binding mode, revealing insight into the mechanism for positive homotropic allostery, or cooperativity. Temperature-dependent analyses reveal that both binding modes imbue increases in bondedness and order toward a more compressed active state. These results provide insight into mechanisms of cooperative TRAP activation and underscore the importance of protein dynamics for ligand binding, ligand release, protein activation, and allostery. © 2013 American Chemical Society.
Cle C.,John Innes Center |
Martin C.,John Innes Center |
Field R.A.,John Innes Center |
Kuzmic P.,BioKin Ltd |
Bornemann S.,John Innes Center
Biocatalysis and Biotransformation | Year: 2010
Strategically important cellular components, such as the cell wall and the starch granule, present surfaces during their biosynthesis and degradation. The enzymology of such surfaces is experimentally challenging and goes well beyond classical solution-state analyses. The kinetics of surface catalysis is complex but tractable. A number of approaches to monitor surface catalysis are reviewed and each is suited to a different biological problem. Particular attention is paid to a method we have recently developed for quantitatively monitoring polysaccharide synthesis on a surface in real time using surface plasmon resonance spectroscopy. This method has many attractive features with the potential to tackle both biological and industrial problems. © 2010 Informa UK Ltd.
Kuzmic P.,BioKin Ltd.
Biochimica et Biophysica Acta - Proteins and Proteomics | Year: 2010
A generalized numerical treatment of steady-state enzyme kinetics is presented. This new approach relies on automatic computer derivation of the underlying mathematical model (a system of simultaneous nonlinear algebraic equations) from a symbolic representation of the reaction mechanism (a system of biochemical equations) provided by the researcher. The method allows experimental biochemists to analyze initial-rate enzyme kinetic data, under the steady-state approximation, without having to use any mathematical equations. An illustrative example is based on the inhibition kinetics of p56lck kinase by an ATP competitive inhibitor. A computer implementation of the new method, in the modified software package DYNAFIT [Kuzmič, P. (1996) Anal. Biochem. 237, 260-273], is freely available to all academic researchers. © 2009.
Wei Y.,Brandeis University |
Wei Y.,Sanford Burnham Institute for Medical Research |
Kuzmic P.,Brandeis University |
Kuzmic P.,BioKin Ltd. |
And 4 more authors.
Biochemistry | Year: 2016
Inosine-5′-monophosphate dehydrogenase (IMPDH) catalyzes the conversion of inosine 5′-monophosphate (IMP) to xanthosine 5′-monophosphate (XMP). The enzyme is an emerging target for antimicrobial therapy. The small molecule inhibitor A110 has been identified as a potent and selective inhibitor of IMPDHs from a variety of pathogenic microorganisms. A recent X-ray crystallographic study reported that the inhibitor binds to the NAD+ cofactor site and forms a ternary complex with IMP. Here we report a pre-steady-state stopped-flow kinetic investigation of IMPDH from Bacillus anthracis designed to assess the kinetic significance of the crystallographic results. Stopped-flow kinetic experiments defined nine microscopic rate constants and two equilibrium constants that characterize both the catalytic cycle and details of the inhibition mechanism. In combination with steady-state initial rate studies, the results show that the inhibitor binds with high affinity (Kd ≈ 50 nM) predominantly to the covalent intermediate on the reaction pathway. Only a weak binding interaction (Kd ≈ 1 μM) is observed between the inhibitor and E·IMP. Thus, the E·IMP·A110 ternary complex, observed by X-ray crystallography, is largely kinetically irrelevant. © 2016 American Chemical Society.
Kuzmic P.,BioKin Ltd.
Analytical Biochemistry | Year: 2011
Optimal experimental designs for the dose-response screening of enzyme inhibitors were studied within the framework of the Box-Lucas theory. If the enzyme concentration E is considered as a fixed constant, an exact two-point D-optimal design consists of a pair of inhibitor concentrations equal to I1=0 and I2=E+K, where K is the apparent inhibition constant. If the enzyme concentration is treated as an adjustable parameter, an empirical three-point D-optimal design consists of three inhibitor concentrations equal to I1=0, I2=E+3K, and I3=0.7E. These results were applied to design optimized, irregularly spaced concentration series for routine inhibitor screening. A heuristic Monte Carlo simulation study confirmed that the optimized dilution series is significantly more efficient than the classic series characterized by a constant dilution ratio. An online calculator to create optimized dilution series is freely available at http://www.biokin.com/design/. © 2011 Elsevier Inc. All rights reserved.
PubMed | BioKin Ltd.
Type: Journal Article | Journal: Analytical biochemistry | Year: 2011
Optimal experimental designs for the dose-response screening of enzyme inhibitors were studied within the framework of the Box-Lucas theory. If the enzyme concentration E is considered as a fixed constant, an exact two-point D-optimal design consists of a pair of inhibitor concentrations equal to I(1)=0 and I(2)=E+K, where K is the apparent inhibition constant. If the enzyme concentration is treated as an adjustable parameter, an empirical three-point D-optimal design consists of three inhibitor concentrations equal to I(1)=0, I(2)=E+3K, and I(3)=0.7E. These results were applied to design optimized, irregularly spaced concentration series for routine inhibitor screening. A heuristic Monte Carlo simulation study confirmed that the optimized dilution series is significantly more efficient than the classic series characterized by a constant dilution ratio. An online calculator to create optimized dilution series is freely available at http://www.biokin.com/design/.
PubMed | BioKin Ltd. and AssayQuant Technologies Inc.
Type: | Journal: Analytical biochemistry | Year: 2016
We propose that the time course of an enzyme reaction following the Michaelis-Menten reaction mechanism can be conveniently described by a newly derived algebraic equation, which includes the Lambert Omega function. Following Northrops ideas [Anal. Biochem.321, 457-461, 1983], the integrated rate equation contains the Michaelis constant (K