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Article ; Online: Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase.

Drago, Victoria N / Devos, Juliette M / Blakeley, Matthew P / Forsyth, V Trevor / Parks, Jerry M / Kovalevsky, Andrey / Mueser, Timothy C

Cell reports. Physical science

2024 Volume 5, Issue 2

Abstract: Pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin ... ...

Abstract	Pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin B
Language	English
Publishing date	2024-02-12
Publishing country	United States
Document type	Journal Article
ISSN	2666-3864
ISSN (online)	2666-3864
DOI	10.1016/j.xcrp.2024.101827
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Article: Equilibration of precipitants in a counter-diffusion apparatus for protein crystallization.

Kober, Umberto A / Ogbuoji, Ebuka A / Hutchinson, John A / Mueser, Timothy C / Schall, Constance A

Journal of applied crystallography

2023 Volume 56, Issue Pt 4, Page(s) 1057–1065

Abstract: A cost-effective capillary dialysis apparatus (Toledo Capillary Box, TCB) developed for biomacromolecule crystal growth in microgravity and unit gravity environments can provide slow equilibration between the precipitant reservoir and capillary solutions, ...

Abstract	A cost-effective capillary dialysis apparatus (Toledo Capillary Box, TCB) developed for biomacromolecule crystal growth in microgravity and unit gravity environments can provide slow equilibration between the precipitant reservoir and capillary solutions, nurturing growth of neutron-diffraction-quality crystals. Under microgravity conditions, mass transfer of precipitants and biomacro-mol-ecules occurs under diffusion-controlled conditions, promoting slow growth and suppressing defect formation. The equilibration of common precipitants (polyethyl-ene glycol and salts such as ammonium sulfate) between capillary and reservoir solutions was measured for capillaries oriented horizontally or vertically with respect to the gravitational field at unit gravity. Precipitants equilibrated less rapidly in the vertical orientation when capillary solution densities were lower than those of the reservoir solutions. A plug filled with agarose gel was introduced in the TCB apparatus for salt precipitants since salts often exhibit relatively high free diffusion. Equilibration of the capillaries with reservoir solutions was significantly delayed for many of the salt precipitants tested. Analytical and semi-analytical models allow the prediction of precipitant equilibration of capillary and reservoir solutions under diffusion-controlled transport and show good agreement with experimental results.
Language	English
Publishing date	2023-06-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2020879-0
ISSN	1600-5767 ; 0021-8898
ISSN (online)	1600-5767
ISSN	0021-8898
DOI	10.1107/S1600576723004958
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Article: Microgravity crystallization of perdeuterated tryptophan synthase for neutron diffraction.

Drago, Victoria N / Devos, Juliette M / Blakeley, Matthew P / Forsyth, V Trevor / Kovalevsky, Andrey Y / Schall, Constance A / Mueser, Timothy C

NPJ microgravity

2022 Volume 8, Issue 1, Page(s) 13

Abstract: Biologically active vitamin ... ...

Abstract	Biologically active vitamin B
Language	English
Publishing date	2022-05-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2823626-9
ISSN	2373-8065
ISSN	2373-8065
DOI	10.1038/s41526-022-00199-3
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Article ; Online: Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase.

Mueser, Timothy C / Drago, Victoria / Kovalevsky, Andrey / Dajnowicz, Steven

Methods in enzymology

2020 Volume 634, Page(s) 333–359

Abstract: Enzyme catalysis is the primary activity in energy and information metabolism and enzyme cofactors are key to the catalytic ability of most enzymes. Pyridoxal 5'-phosphate (PLP) cofactor, derived from Vitamin B6, is widely distributed in nature and has ... ...

Abstract	Enzyme catalysis is the primary activity in energy and information metabolism and enzyme cofactors are key to the catalytic ability of most enzymes. Pyridoxal 5'-phosphate (PLP) cofactor, derived from Vitamin B6, is widely distributed in nature and has significant latitude in catalytic diversity. X-ray crystallography has revealed the structures of diverse PLP dependent enzymes from multiple families. But these structures are incomplete, lacking the positions of protons essential for understanding enzymatic mechanisms. Here, we review the diversity of PLP and discuss the use of neutron crystallography and joint X-ray/neutron refinement of Fold Type I aspartate aminotransferase to visualize the positions of protons in both the internal and external aldimine forms. Strategies used to prepare extremely large crystals required for neutron diffraction and the approach to data refinement including the PLP cofactor are discussed. The observed positions of protons, including one located in a previously unknown low-barrier hydrogen bond, have been used to create more accurate models for computational analysis. The results revealed a new mechanism for the transaminase reaction where hyperconjugation is key to reducing the energy barrier which finally provides a clear explanation of the Dunathan alignment.
MeSH term(s)	Aspartate Aminotransferases ; Catalysis ; Crystallography, X-Ray ; Phosphates ; Pyridoxal Phosphate
Chemical Substances	Phosphates ; Pyridoxal Phosphate (5V5IOJ8338) ; Aspartate Aminotransferases (EC 2.6.1.1)
Language	English
Publishing date	2020-02-13
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/bs.mie.2020.01.009
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Article: An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction.

Drago, Victoria N / Dajnowicz, Steven / Parks, Jerry M / Blakeley, Matthew P / Keen, David A / Coquelle, Nicolas / Weiss, Kevin L / Gerlits, Oksana / Kovalevsky, Andrey / Mueser, Timothy C

Chemical science

2022 Volume 13, Issue 34, Page(s) 10057–10065

Abstract: Pyridoxal 5'-phosphate (PLP)-dependent enzymes have been extensively studied for their ability to fine-tune PLP cofactor electronics to promote a wide array of chemistries. Neutron crystallography offers a straightforward approach to studying the ... ...

Abstract	Pyridoxal 5'-phosphate (PLP)-dependent enzymes have been extensively studied for their ability to fine-tune PLP cofactor electronics to promote a wide array of chemistries. Neutron crystallography offers a straightforward approach to studying the electronic states of PLP and the electrostatics of enzyme active sites, responsible for the reaction specificities, by enabling direct visualization of hydrogen atom positions. Here we report a room-temperature joint X-ray/neutron structure of aspartate aminotransferase (AAT) with pyridoxamine 5'-phosphate (PMP), the cofactor product of the first half reaction catalyzed by the enzyme. Between PMP N
Language	English
Publishing date	2022-08-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d2sc02285k
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Article ; Online: Substrate Binding Stiffens Aspartate Aminotransferase by Altering the Enzyme Picosecond Vibrational Dynamics.

Dajnowicz, Steven / Cheng, Yongqiang / Daemen, Luke L / Weiss, Kevin L / Gerlits, Oksana / Mueser, Timothy C / Kovalevsky, Andrey

ACS omega

2020 Volume 5, Issue 30, Page(s) 18787–18797

Abstract: Protein dynamics on various time scales from femtoseconds to milliseconds impacts biological function by driving proteins to conformations conducive to ligand binding and creating functional states in enzyme catalysis. Neutron vibrational spectroscopy ... ...

Abstract	Protein dynamics on various time scales from femtoseconds to milliseconds impacts biological function by driving proteins to conformations conducive to ligand binding and creating functional states in enzyme catalysis. Neutron vibrational spectroscopy carried out by measuring inelastic neutron scattering from protein molecules in combination with molecular simulations has the unique ability of detecting and visualizing changes in the picosecond protein vibrational dynamics due to ligand binding. Here we present neutron vibrational spectra of a homodimeric pyridoxal 5'-phosphate-dependent enzyme, aspartate aminotransferase, obtained from the open internal aldimine and closed external aldimine conformational states. We observe that in the external aldimine state the protein structure stiffens relative to the internal aldimine state, indicating rigidified vibrational dynamics on the picosecond time scale in the low-frequency regime of 5-50 cm
Language	English
Publishing date	2020-07-23
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.0c01900
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Article ; Online: Substrate Binding Stiffens Aspartate Aminotransferase by Altering the Enzyme Picosecond Vibrational Dynamics

Steven Dajnowicz / Yongqiang Cheng / Luke L. Daemen / Kevin L. Weiss / Oksana Gerlits / Timothy C. Mueser / Andrey Kovalevsky

ACS Omega, Vol 5, Iss 30, Pp 18787-

2020 Volume 18797

Keywords	Chemistry ; QD1-999
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	American Chemical Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin.

Delgadillo, Roberto F / Mueser, Timothy C / Zaleta-Rivera, Kathia / Carnes, Katie A / González-Valdez, José / Parkhurst, Lawrence J

PloS one

2019 Volume 14, Issue 2, Page(s) e0204194

Abstract: The high affinity (KD ~ 10-15 M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that ... ...

Abstract	The high affinity (KD ~ 10-15 M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (kon) is approximately diffusion limited (109 M-1s-1) but recent single molecule and surface binding studies indicate that they are slower than expected (105 to 107 M-1s-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic cycle describes the complex formation, and if there are any functional differences between avidin and streptavidin. We have studied the biotin association by two stopped-flow methodologies using labeled and unlabeled probes: I) fluorescent probes attached to biotin and biocytin; and II) unlabeled biotin and HABA, 2-(4'-hydroxyazobenzene)-benzoic acid. Both native avidin and streptavidin are homo-tetrameric and the association data show no cooperativity between the binding sites. The kon values of streptavidin are faster than avidin but slower than expected for a diffusion limited reaction in both complexes. Moreover, the Arrhenius plots of the kon values revealed strong temperature dependence with large activation energies (6-15 kcal/mol) that do not correspond to a diffusion limited process (3-4 kcal/mol). Accordingly, we propose a simple reaction model with a single transition state for non-immobilized reactants whose forward thermodynamic parameters complete the thermodynamic cycle, in agreement with previously reported studies. Our new understanding and description of the kinetics, thermodynamics, and spectroscopic parameters for these complexes will help to improve purification efficiencies, molecule detection, and drug screening assays or find new applications.
MeSH term(s)	Avidin/chemistry ; Azo Compounds/chemistry ; Binding Sites ; Biotin/chemistry ; DNA/chemistry ; Diffusion ; Fluorescent Dyes ; Kinetics ; Lysine/analogs & derivatives ; Lysine/chemistry ; Protein Binding ; Solutions/chemistry ; Streptavidin/chemistry ; Thermodynamics
Chemical Substances	Azo Compounds ; Fluorescent Dyes ; Solutions ; Avidin (1405-69-2) ; HABA (1634-82-8) ; Biotin (6SO6U10H04) ; DNA (9007-49-2) ; Streptavidin (9013-20-1) ; biocytin (G6D6147J22) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2019-02-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0204194
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Article ; Online: Direct evidence that an extended hydrogen-bonding network influences activation of pyridoxal 5'-phosphate in aspartate aminotransferase.

Dajnowicz, Steven / Parks, Jerry M / Hu, Xiche / Gesler, Korie / Kovalevsky, Andrey Y / Mueser, Timothy C

The Journal of biological chemistry

2017 Volume 292, Issue 14, Page(s) 5970–5980

Abstract: Pyridoxal 5'-phosphate (PLP) is a fundamental, multifunctional enzyme cofactor used to catalyze a wide variety of chemical reactions involved in amino acid metabolism. PLP-dependent enzymes optimize specific chemical reactions by modulating the ... ...

Abstract	Pyridoxal 5'-phosphate (PLP) is a fundamental, multifunctional enzyme cofactor used to catalyze a wide variety of chemical reactions involved in amino acid metabolism. PLP-dependent enzymes optimize specific chemical reactions by modulating the electronic states of PLP through distinct active site environments. In aspartate aminotransferase (AAT), an extended hydrogen bond network is coupled to the pyridinyl nitrogen of the PLP, influencing the electrophilicity of the cofactor. This network, which involves residues Asp-222, His-143, Thr-139, His-189, and structural waters, is located at the edge of PLP opposite the reactive Schiff base. We demonstrate that this hydrogen bond network directly influences the protonation state of the pyridine nitrogen of PLP, which affects the rates of catalysis. We analyzed perturbations caused by single- and double-mutant variants using steady-state kinetics, high resolution X-ray crystallography, and quantum chemical calculations. Protonation of the pyridinyl nitrogen to form a pyridinium cation induces electronic delocalization in the PLP, which correlates with the enhancement in catalytic rate in AAT. Thus, PLP activation is controlled by the proximity of the pyridinyl nitrogen to the hydrogen bond microenvironment. Quantum chemical calculations indicate that Asp-222, which is directly coupled to the pyridinyl nitrogen, increases the p
MeSH term(s)	Animals ; Aspartate Aminotransferases/chemistry ; Aspartate Aminotransferases/genetics ; Aspartate Aminotransferases/metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Protein Domains ; Pyridoxal Phosphate/chemistry ; Pyridoxal Phosphate/genetics ; Pyridoxal Phosphate/metabolism ; Sus scrofa
Chemical Substances	Pyridoxal Phosphate (5V5IOJ8338) ; Aspartate Aminotransferases (EC 2.6.1.1)
Language	English
Publishing date	2017-02-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M116.774588
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Article ; Online: Models for the binary complex of bacteriophage T4 gp59 helicase loading protein: gp32 single-stranded DNA-BINDING protein and ternary complex with pseudo-Y junction DNA.

Hinerman, Jennifer M / Dignam, J David / Mueser, Timothy C

The Journal of biological chemistry

2012 Volume 287, Issue 22, Page(s) 18608–18617

Abstract: ... Jones, C. E., Lai, X., Brister, J. R., Mueser, T. C., Nossal, N. G., and Hinton, D. M. (2012) J. Biol ... that the gp32 protein C-terminal A-domain is essential for protein-protein interaction in the absence of DNA ...

Abstract	Bacteriophage T4 gp59 helicase assembly protein (gp59) is required for loading of gp41 replicative helicase onto DNA protected by gp32 single-stranded DNA-binding protein. The gp59 protein recognizes branched DNA structures found at replication and recombination sites. Binding of gp32 protein (full-length and deletion constructs) to gp59 protein measured by isothermal titration calorimetry demonstrates that the gp32 protein C-terminal A-domain is essential for protein-protein interaction in the absence of DNA. Sedimentation velocity experiments with gp59 protein and gp32ΔB protein (an N-terminal B-domain deletion) show that these proteins are monomers but form a 1:1 complex with a dissociation constant comparable with that determined by isothermal titration calorimetry. Small angle x-ray scattering (SAXS) studies indicate that the gp59 protein is a prolate monomer, consistent with the crystal structure and hydrodynamic properties determined from sedimentation velocity experiments. SAXS experiments also demonstrate that gp32ΔB protein is a prolate monomer with an elongated A-domain protruding from the core. Fitting structures of gp59 protein and the gp32 core into the SAXS-derived molecular envelope supports a model for the gp59 protein-gp32ΔB protein complex. Our earlier work demonstrated that gp59 protein attracts full-length gp32 protein to pseudo-Y junctions. A model of the gp59 protein-DNA complex, modified to accommodate new SAXS data for the binary complex together with mutational analysis of gp59 protein, is presented in the accompanying article (Dolezal, D., Jones, C. E., Lai, X., Brister, J. R., Mueser, T. C., Nossal, N. G., and Hinton, D. M. (2012) J. Biol. Chem. 287, 18596-18607).
MeSH term(s)	DNA, Viral/metabolism ; DNA-Binding Proteins/metabolism ; Electrophoresis, Agar Gel ; Models, Molecular ; Scattering, Small Angle ; Ultracentrifugation ; Viral Proteins/metabolism ; X-Ray Diffraction
Chemical Substances	DNA, Viral ; DNA-Binding Proteins ; Viral Proteins ; gene 59 protein, Enterobacteria phage T4
Language	English
Publishing date	2012-04-05
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M111.333476
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