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Article ; Online: Molecular dynamics simulations demonstrate that non-ideal mixing dominates subsaturation organic aerosol hygroscopicity.

Roston, Daniel

Physical chemistry chemical physics : PCCP

2021 Volume 23, Issue 15, Page(s) 9218–9227

Abstract: The microscopic properties that determine hygroscopic behavior are complex. The importance of hygroscopicity to many areas, and particularly atmospheric chemistry, in terms of aerosol growth and cloud nucleation, mandate the need for robust models to ... ...

Abstract	The microscopic properties that determine hygroscopic behavior are complex. The importance of hygroscopicity to many areas, and particularly atmospheric chemistry, in terms of aerosol growth and cloud nucleation, mandate the need for robust models to understand this behavior. Toward this end, we have employed molecular dynamics simulations to calculate hygroscopicity from atomistic models using free energy perturbation. We find that currently available force fields may not be well-suited to modeling the extreme environments of aerosol particles. Nonetheless, the results illuminate some shortcomings in our current understanding of hygroscopic growth and cloud nucleation. The most widely used model of hygroscopicity, κ-Köhler Theory (κKT), breaks down in the case of deviations from ideal solution behavior and empirical adjustments within the simplified framework cannot account for non-ideal behavior. A revised model that incorporates non-ideal mixing rescues the general framework of κKT and allows us to understand our simulation results as well as the behavior of atmospheric aerosols over the full range of humidity. The revised model shows that non-ideal mixing dominates hygroscopic growth at subsaturation humidity. Thus, a model based on ideal mixing will fail to predict subsaturation growth from cloud condensation nucleus (CCN) activation or vice versa; a single parameter model for hygroscopicity will generally be insufficient to extrapolate across wide ranges of humidity. We argue that in many cases, when data are limited to subsaturation humidity, an empirical model for non-ideal mixing may be more successful than one for ideal mixing.
Language	English
Publishing date	2021-04-21
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d1cp00245g
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Bacterial H-NS contacts DNA at the same irregularly spaced sites in both bridged and hemi-sequestered linear filaments.

Shen, Beth A / Hustmyer, Christine M / Roston, Daniel / Wolfe, Michael B / Landick, Robert

iScience

2022 Volume 25, Issue 6, Page(s) 104429

Abstract: Gene silencing in bacteria is mediated by chromatin proteins, of ... ...

Abstract	Gene silencing in bacteria is mediated by chromatin proteins, of which
Language	English
Publishing date	2022-05-18
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.104429
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Article ; Online: Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase.

Roston, Daniel / Demapan, Darren / Cui, Qiang

Proceedings of the National Academy of Sciences of the United States of America

2019 Volume 116, Issue 50, Page(s) 25048–25056

Abstract: Transphosphorylation of nucleotide triphosphates is the central reaction in DNA replication by DNA polymerase as well as many other biological processes. Despite its importance, the microscopic chemical mechanism of transphosphorylation of nucleotide ... ...

Abstract	Transphosphorylation of nucleotide triphosphates is the central reaction in DNA replication by DNA polymerase as well as many other biological processes. Despite its importance, the microscopic chemical mechanism of transphosphorylation of nucleotide triphosphates is, in most cases, unknown. Here we use extensive simulations of DNA polymerase η to test mechanistic hypotheses. We systematically survey the reactive space by calculating 2D free-energy surfaces for 10 different plausible mechanisms that have been proposed. We supplement these free-energy surfaces with calculations of pK
MeSH term(s)	DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/metabolism ; Magnesium/chemistry ; Magnesium/metabolism ; Metabolic Networks and Pathways ; Molecular Dynamics Simulation ; Nucleotides/chemistry ; Nucleotides/metabolism ; Thermodynamics ; Water/chemistry ; Water/metabolism
Chemical Substances	Nucleotides ; Water (059QF0KO0R) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2019-11-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1914613116
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Article ; Online: Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects.

Roston, Daniel / Cui, Qiang

Journal of the American Chemical Society

2016 Volume 138, Issue 36, Page(s) 11946–11957

Abstract: Enzymes are powerful catalysts, and a thorough understanding of the sources of their catalytic power will facilitate many medical and industrial applications. Here we have studied the catalytic mechanism of alkaline phosphatase (AP), which is one of the ... ...

Abstract	Enzymes are powerful catalysts, and a thorough understanding of the sources of their catalytic power will facilitate many medical and industrial applications. Here we have studied the catalytic mechanism of alkaline phosphatase (AP), which is one of the most catalytically proficient enzymes known. We have used quantum mechanics calculations and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to model a variety of isotope effects relevant to the reaction of AP. We have calculated equilibrium isotope effects (EIEs), binding isotope effects (BIEs), and kinetic isotope effects (KIEs) for a range of phosphate mono- and diester substrates. The results agree well with experimental values, but the model for the reaction's transition state (TS) differs from the original interpretation of those experiments. Our model indicates that isotope effects on binding make important contributions to measured KIEs on V/K, which complicated interpretation of the measured values. Our results provide a detailed interpretation of the measured isotope effects and make predictions that can test the proposed model. The model indicates that the substrate is deformed in the ground state (GS) of the reaction and partially resembles the TS. The highly preorganized active site preferentially binds conformations that resemble the TS and not the GS, which induces the substrate to adapt to the enzyme, rather than the other way around-as with classic "induced fit" models. The preferential stabilization of the TS over the GS is what lowers the barrier to the chemical step.
MeSH term(s)	Alkaline Phosphatase/chemistry ; Alkaline Phosphatase/metabolism ; Catalytic Domain ; Kinetics ; Models, Molecular ; Oxygen Isotopes ; Protein Binding
Chemical Substances	Oxygen Isotopes ; Alkaline Phosphatase (EC 3.1.3.1)
Language	English
Publishing date	2016-08-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.6b07347
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Article: The Sorghum bicolor Root Exudate Sorgoleone Shapes Bacterial Communities and Delays Network Formation.

Wang, Peng / Chai, Yen Ning / Roston, Rebecca / Dayan, Franck E / Schachtman, Daniel P

mSystems

2021 Volume 6, Issue 2

Abstract: Primary and secondary metabolites exuded from roots are key drivers of root-soil microbe interactions that contribute to the structure and function of microbial communities. Studies with model plants have begun to reveal the complex interactions between ... ...

Abstract	Primary and secondary metabolites exuded from roots are key drivers of root-soil microbe interactions that contribute to the structure and function of microbial communities. Studies with model plants have begun to reveal the complex interactions between root exudates and soil microbes, but little is known about the influence of specialized exudates from crop plants. The aims of this work were to understand whether sorgoleone, a unique lipophilic secondary benzoquinone exuded only from the root hairs of sorghum, influences belowground microbial community structure in the field, to assess the effect of purified sorgoleone on the cultured bacteria from field soils, and to determine whether sorgoleone inhibits nitrification under field conditions. Studies were conducted comparing wild-type sorghum and lines with genetically reduced sorgoleone exudation. In the soil near roots and rhizosphere, sorgoleone influenced microbial community structure as measured by β-diversity and network analysis. Under greenhouse conditions, the soil nitrogen content was an important factor in determining the impacts of sorgoleone. Sorgoleone delayed the formation of the bacterial and archaeal networks early in plant development and only inhibited nitrification at specific sampling times under field conditions. Sorgoleone was also shown to both inhibit and promote cultured bacterial isolate growth in laboratory tests. These findings provide new insights into the role of secondary metabolites in shaping the composition and function of the sorghum root-associated bacterial microbiomes. Understanding how root exudates modify soil microbiomes may potentially unlock an important tool for enhancing crop sustainability and yield in our changing environment.
Language	English
Publishing date	2021-03-16
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00749-20
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Article ; Online: Bacterial H-NS contacts DNA at the same irregularly spaced sites in both bridged and hemi-sequestered linear filaments

Beth A. Shen / Christine M. Hustmyer / Daniel Roston / Michael B. Wolfe / Robert Landick

iScience, Vol 25, Iss 6, Pp 104429- (2022)

2022

Abstract: Summary: Gene silencing in bacteria is mediated by chromatin proteins, of which Escherichia coli H-NS is a paradigmatic example. H-NS forms nucleoprotein filaments with either one or two DNA duplexes. However, the structures, arrangements of DNA-binding ... ...

Abstract	Summary: Gene silencing in bacteria is mediated by chromatin proteins, of which Escherichia coli H-NS is a paradigmatic example. H-NS forms nucleoprotein filaments with either one or two DNA duplexes. However, the structures, arrangements of DNA-binding domains (DBDs), and positions of DBD–DNA contacts in linear and bridged filaments are uncertain. To characterize the H-NS DBD contacts that silence transcription by RNA polymerase, we combined ·OH footprinting, molecular dynamics, statistical modeling, and DBD mapping using a chemical nuclease (Fe2+-EDTA) tethered to the DBDs (TEN-map). We find that H-NS DBDs contact DNA at indistinguishable locations in bridged or linear filaments and that the DBDs vary in orientation and position with ∼10-bp average spacing. Our results support a hemi-sequestration model of linear-to-bridged H-NS switching. Linear filaments able to inhibit only transcription initiation switch to bridged filaments able to inhibit both initiation and elongation using the same irregularly spaced DNA contacts.
Keywords	Biological sciences ; Molecular biology ; Molecular mechanism of gene regulation ; Science ; Q
Subject code	612
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects

Roston, Daniel / Cui Qiang

Journal of the American Chemical Society. 2016 Sept. 14, v. 138, no. 36

2016

Abstract	Enzymes are powerful catalysts, and a thorough understanding of the sources of their catalytic power will facilitate many medical and industrial applications. Here we have studied the catalytic mechanism of alkaline phosphatase (AP), which is one of the most catalytically proficient enzymes known. We have used quantum mechanics calculations and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to model a variety of isotope effects relevant to the reaction of AP. We have calculated equilibrium isotope effects (EIEs), binding isotope effects (BIEs), and kinetic isotope effects (KIEs) for a range of phosphate mono- and diester substrates. The results agree well with experimental values, but the model for the reactionâs transition state (TS) differs from the original interpretation of those experiments. Our model indicates that isotope effects on binding make important contributions to measured KIEs on V/K, which complicated interpretation of the measured values. Our results provide a detailed interpretation of the measured isotope effects and make predictions that can test the proposed model. The model indicates that the substrate is deformed in the ground state (GS) of the reaction and partially resembles the TS. The highly preorganized active site preferentially binds conformations that resemble the TS and not the GS, which induces the substrate to adapt to the enzyme, rather than the other way aroundî¸as with classic âinduced fitâ models. The preferential stabilization of the TS over the GS is what lowers the barrier to the chemical step.
Keywords	active sites ; alkaline phosphatase ; catalysts ; industrial applications ; isotopes ; models ; oxygen ; phosphates ; prediction ; quantum mechanics
Language	English
Dates of publication	2016-0914
Size	p. 11946-11957.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021%2Fjacs.6b07347
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations.

Roston, Daniel / Lu, Xiya / Fang, Dong / Demapan, Darren / Cui, Qiang

Methods in enzymology

2018 Volume 607, Page(s) 53–90

Abstract: We discuss the application of quantum mechanics/molecular mechanics (QM/MM) free energy simulations to the analysis of phosphoryl transfers catalyzed by two enzymes: alkaline phosphatase and myosin. We focus on the nature of the transition state and the ... ...

Abstract	We discuss the application of quantum mechanics/molecular mechanics (QM/MM) free energy simulations to the analysis of phosphoryl transfers catalyzed by two enzymes: alkaline phosphatase and myosin. We focus on the nature of the transition state and the issue of mechanochemical coupling, respectively, in the two enzymes. The results illustrate unique insights that emerged from the QM/MM simulations, especially concerning the interpretation of experimental data regarding the nature of enzymatic transition states and coupling between global structural transition and catalysis in the active site. We also highlight a number of technical issues worthy of attention when applying QM/MM free energy simulations, and comment on a number of technical and mechanistic issues that require further studies.
MeSH term(s)	Alkaline Phosphatase/chemistry ; Alkaline Phosphatase/metabolism ; Molecular Dynamics Simulation ; Myosins/chemistry ; Myosins/metabolism ; Quantum Theory
Chemical Substances	Alkaline Phosphatase (EC 3.1.3.1) ; Myosins (EC 3.6.4.1)
Language	English
Publishing date	2018-08-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1557-7988 ; 0076-6879
ISSN (online)	1557-7988
ISSN	0076-6879
DOI	10.1016/bs.mie.2018.05.005
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Article ; Online: Predicting transcriptional responses to cold stress across plant species.

Meng, Xiaoxi / Liang, Zhikai / Dai, Xiuru / Zhang, Yang / Mahboub, Samira / Ngu, Daniel W / Roston, Rebecca L / Schnable, James C

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 10

Abstract: Although genome-sequence assemblies are available for a growing number of plant species, gene-expression responses to stimuli have been cataloged for only a subset of these species. Many genes show altered transcription patterns in response to abiotic ... ...

Abstract	Although genome-sequence assemblies are available for a growing number of plant species, gene-expression responses to stimuli have been cataloged for only a subset of these species. Many genes show altered transcription patterns in response to abiotic stresses. However, orthologous genes in related species often exhibit different responses to a given stress. Accordingly, data on the regulation of gene expression in one species are not reliable predictors of orthologous gene responses in a related species. Here, we trained a supervised classification model to identify genes that transcriptionally respond to cold stress. A model trained with only features calculated directly from genome assemblies exhibited only modest decreases in performance relative to models trained by using genomic, chromatin, and evolution/diversity features. Models trained with data from one species successfully predicted which genes would respond to cold stress in other related species. Cross-species predictions remained accurate when training was performed in cold-sensitive species and predictions were performed in cold-tolerant species and vice versa. Models trained with data on gene expression in multiple species provided at least equivalent performance to models trained and tested in a single species and outperformed single-species models in cross-species prediction. These results suggest that classifiers trained on stress data from well-studied species may suffice for predicting gene-expression patterns in related, less-studied species with sequenced genomes.
MeSH term(s)	Cold-Shock Response ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Models, Genetic ; Poaceae/genetics ; Poaceae/metabolism ; Species Specificity ; Transcription, Genetic
Language	English
Publishing date	2021-02-23
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2026330118
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Article ; Online: A critical test of the "tunneling and coupled motion" concept in enzymatic alcohol oxidation.

Roston, Daniel / Kohen, Amnon

Journal of the American Chemical Society

2013 Volume 135, Issue 37, Page(s) 13624–13627

Abstract: The physical mechanism of C-H bond activation by enzymes is the subject of intense study, and we have tested the predictions of two competing models for C-H activation in the context of alcohol dehydrogenase. The kinetic isotope effects (KIEs) in this ... ...

Abstract	The physical mechanism of C-H bond activation by enzymes is the subject of intense study, and we have tested the predictions of two competing models for C-H activation in the context of alcohol dehydrogenase. The kinetic isotope effects (KIEs) in this enzyme have previously suggested a model of quantum mechanical tunneling and coupled motion of primary (1°) and secondary (2°) hydrogens. Here we measure the 2° H/T KIEs with both H and D at the 1° position and find that the 2° KIE is significantly deflated with D-transfer, consistent with the predictions of recent Marcus-like models of H-transfer. The results suggest that the fast dynamics of H-tunneling result in a 1° isotope effect on the structure of the tunneling ready state: the trajectory of D-transfer goes through a shorter donor-acceptor distance than that of H-transfer.
MeSH term(s)	Alcohol Dehydrogenase/chemistry ; Alcohol Dehydrogenase/metabolism ; Benzyl Alcohol/chemistry ; Models, Molecular ; Oxidation-Reduction
Chemical Substances	Alcohol Dehydrogenase (EC 1.1.1.1) ; Benzyl Alcohol (LKG8494WBH)
Language	English
Publishing date	2013-09-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/ja405917m
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