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Article ; Online: The

Parthasarathy, Anutthaman / Adams, Lily E / Savka, Francisco C / Hudson, André O

Plant direct

2019 Volume 3, Issue 9, Page(s) e00171

Abstract: The aminotransferase gene family in the model ... ...

Abstract	The aminotransferase gene family in the model plant
Language	English
Publishing date	2019-09-18
Publishing country	England
Document type	Journal Article
ISSN	2475-4455
ISSN (online)	2475-4455
DOI	10.1002/pld3.171
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Article ; Online: Efficacy of different AV7909 dose regimens in a nonclinical model of pulmonary anthrax.

Henning, Lisa / Anderson, Michael / Triplett, Cheryl / Smith, Tammy / Boyce, Kevin / Hendey, Lindsay / Ridenour, Alex / Eng, Jason / Schaeufele, David / Wilson, Ehran / Sabourin, Carol L / Adams, Lily E / Babas, Tahar / Parish, Lindsay / Wolfe, Daniel

Human vaccines & immunotherapeutics

2023 Volume 19, Issue 3, Page(s) 2290345

Abstract: Pulmonary anthrax caused by exposure to ... ...

Abstract	Pulmonary anthrax caused by exposure to inhaled
MeSH term(s)	Adult ; Humans ; Animals ; Guinea Pigs ; Anthrax/prevention & control ; Anthrax Vaccines ; Antibodies, Bacterial ; Bacillus anthracis ; Antibodies, Neutralizing ; Antigens, Bacterial
Chemical Substances	Anthrax Vaccines ; Antibodies, Bacterial ; Antibodies, Neutralizing ; Antigens, Bacterial
Language	English
Publishing date	2023-12-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2664176-8
ISSN	2164-554X ; 2164-5515
ISSN (online)	2164-554X
ISSN	2164-5515
DOI	10.1080/21645515.2023.2290345
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Article: The Arabidopsis thaliana gene annotated by the locus tag At3g08860 encodes alanine aminotransferase

Parthasarathy, Anutthaman / Adams, Lily E. / Savka, Francisco C. / Hudson, André O.

Plant direct. 2019 Sept., v. 3, no. 9

2019

Abstract: The aminotransferase gene family in the model plant Arabidopsis thaliana consists of 44 genes, eight of which are suggested to be alanine aminotransferases. One of the putative alanine aminotransferases genes, At3g08860, was attributed the function of ... ...

Abstract	The aminotransferase gene family in the model plant Arabidopsis thaliana consists of 44 genes, eight of which are suggested to be alanine aminotransferases. One of the putative alanine aminotransferases genes, At3g08860, was attributed the function of alanine:glyoxylate aminotransferase/β‐alanine:pyruvate aminotransferase based on the analysis of gene expression networks and homology to other β‐alanine aminotransferases in plants. It was earlier demonstrated that At3g08860 is specifically upregulated in response to osmotic stress, but not other stresses (β‐alanine is an osmoprotectant in plants). Furthermore, it was shown that the expression of At3g08860 is highly coordinated with the genes of the uracil degradation pathway leading to the non‐proteinogenic amino acid β‐alanine. These evidence were suggestive of the involvement of At3g08860 in β‐alanine metabolism. However, direct experimental evidence for the function of At3g08860 was lacking, and therefore, the goal of this study was to elucidate the function of the uncharacterized aminotransferase annotated by the locus tag At3g08860. The cDNA of At3g08860 was demonstrated to functionally complement two E. coli mutants auxotrophic for the amino acids, L‐alanine (proteinogenic) and β‐alanine (non‐proteinogenic). Enzyme activity using purified recombinant At3g08860 further demonstrated that the enzyme is endowed with L‐alanine:glyoxylate aminotransferase activity.
Keywords	Arabidopsis thaliana ; Escherichia coli ; alanine ; alanine transaminase ; auxotrophs ; enzyme activity ; gene expression ; genes ; loci ; metabolism ; osmotic stress ; osmotolerance ; uracil
Language	English
Dates of publication	2019-09
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ISSN	2475-4455
DOI	10.1002/pld3.171
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Critical ACE2 Determinants of SARS-CoV-2 and Group 2B Coronavirus Infection and Replication.

Adams, Lily E / Dinnon, Kenneth H / Hou, Yixuan J / Sheahan, Timothy P / Heise, Mark T / Baric, Ralph S

mBio

2021 Volume 12, Issue 2

Abstract: The angiotensin-converting enzyme 2 (ACE2) receptor is a major severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) host range determinant, and understanding SARS-CoV-2-ACE2 interactions will provide important insights into COVID-19 pathogenesis ... ...

Abstract	The angiotensin-converting enzyme 2 (ACE2) receptor is a major severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) host range determinant, and understanding SARS-CoV-2-ACE2 interactions will provide important insights into COVID-19 pathogenesis and animal model development. SARS-CoV-2 cannot infect mice due to incompatibility between its receptor binding domain and the murine ACE2 receptor. Through molecular modeling and empirical
MeSH term(s)	Amino Acid Sequence ; Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; Animals ; Betacoronavirus/metabolism ; Betacoronavirus/physiology ; Binding Sites ; COVID-19/virology ; Cell Line ; Coronavirus Infections/virology ; Host Specificity ; Humans ; Mice ; Models, Molecular ; Mutation ; Protein Binding ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; SARS-CoV-2/metabolism ; SARS-CoV-2/physiology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Virus Replication
Chemical Substances	Recombinant Proteins ; Spike Glycoprotein, Coronavirus ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.03149-20
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Article ; Online: DROIDS 3.0-Detecting Genetic and Drug Class Variant Impact on Conserved Protein Binding Dynamics.

Babbitt, Gregory A / Fokoue, Ernest P / Evans, Joshua R / Diller, Kyle I / Adams, Lily E

Biophysical journal

2019 Volume 118, Issue 3, Page(s) 541–551

Abstract: The application of statistical methods to comparatively framed questions about the molecular dynamics (MD) of proteins can potentially enable investigations of biomolecular function beyond the current sequence and structural methods in bioinformatics. ... ...

Abstract	The application of statistical methods to comparatively framed questions about the molecular dynamics (MD) of proteins can potentially enable investigations of biomolecular function beyond the current sequence and structural methods in bioinformatics. However, the chaotic behavior in single MD trajectories requires statistical inference that is derived from large ensembles of simulations representing the comparative functional states of a protein under investigation. Meaningful interpretation of such complex forms of big data poses serious challenges to users of MD. Here, we announce Detecting Relative Outlier Impacts from Molecular Dynamic Simulation (DROIDS) 3.0, a method and software package for comparative protein dynamics that includes maxDemon 1.0, a multimethod machine learning application that trains on large ensemble comparisons of concerted protein motions in opposing functional states generated by DROIDS and deploys learned classifications of these states onto newly generated MD simulations. Local canonical correlations in learning patterns generated from independent, yet identically prepared, MD validation runs are used to identify regions of functionally conserved protein dynamics. The subsequent impacts of genetic and/or drug class variants on conserved dynamics can also be analyzed by deploying the classifiers on variant MD simulations and quantifying how often these altered protein systems display opposing functional states. Here, we present several case studies of complex changes in functional protein dynamics caused by temperature, genetic mutation, and binding interactions with nucleic acids and small molecules. We demonstrate that our machine learning algorithm can properly identify regions of functionally conserved dynamics in ubiquitin and TATA-binding protein (TBP). We quantify the impact of genetic variation in TBP and drug class variation targeting the ATP-binding region of Hsp90 on conserved dynamics. We identify regions of conserved dynamics in Hsp90 that connect the ATP binding pocket to other functional regions. We also demonstrate that dynamic impacts of various Hsp90 inhibitors rank accordingly with how closely they mimic natural ATP binding.
MeSH term(s)	Computational Biology ; Molecular Dynamics Simulation ; Pharmaceutical Preparations ; Protein Binding ; Protein Conformation ; Proteins/metabolism
Chemical Substances	Pharmaceutical Preparations ; Proteins
Language	English
Publishing date	2019-12-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2019.12.008
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Article: Non-neutralizing SARS-CoV-2 N-terminal domain antibodies protect mice against severe disease using Fc-mediated effector functions.

Pierre, Camille N / Adams, Lily E / Anasti, Kara / Goodman, Derrick / Stanfield-Oakley, Sherry / Powers, John M / Li, Dapeng / Rountree, Wes / Wang, Yunfei / Edwards, Robert J / Munir Alam, S / Ferrari, Guido / Tomaras, Georgia D / Haynes, Barton F / Baric, Ralph S / Saunders, Kevin O

bioRxiv : the preprint server for biology

2023

Abstract: Antibodies perform both neutralizing and non-neutralizing effector functions that protect against certain pathogen-induced diseases. A human antibody directed at the SARS-CoV-2 Spike N-terminal domain (NTD), DH1052, was recently shown to be non- ... ...

Abstract	Antibodies perform both neutralizing and non-neutralizing effector functions that protect against certain pathogen-induced diseases. A human antibody directed at the SARS-CoV-2 Spike N-terminal domain (NTD), DH1052, was recently shown to be non-neutralizing yet it protected mice and cynomolgus macaques from severe disease. The mechanisms of this non-neutralizing antibody-mediated protection are unknown. Here we show that Fc effector functions mediate non-neutralizing antibody (non-nAb) protection against SARS-CoV-2 MA10 viral challenge in mice. Though non-nAb infusion did not suppress infectious viral titers in the lung as potently as NTD neutralizing antibody (nAb) infusion, disease markers including gross lung discoloration were similar in nAb and non-nAb groups. Fc functional knockout substitutions abolished non-nAb protection and increased viral titers in the nAb group. Finally, Fc enhancement increased non-nAb protection relative to WT, supporting a positive association between Fc functionality and degree of protection in SARS-CoV-2 infection. This study demonstrates that non-nAbs can utilize Fc-mediated mechanisms to lower viral load and prevent lung damage due to coronavirus infection.
Language	English
Publishing date	2023-07-26
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.25.550460
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Article ; Online: Generation of Mature DENVs via Genetic Modification and Directed Evolution.

Tse, Longping V / Meganck, Rita M / Dong, Stephanie / Adams, Lily E / White, Laura J / Mallory, Michael L / Jadi, Ramesh / de Silva, Aravinda M / Baric, Ralph S

mBio

2022 Volume 13, Issue 3, Page(s) e0038622

Abstract: Maturation of dengue viruses (DENVs) alters the structure, immunity, and infectivity of the virion and highly mature particles represent the dominant ... ...

Abstract	Maturation of dengue viruses (DENVs) alters the structure, immunity, and infectivity of the virion and highly mature particles represent the dominant form
MeSH term(s)	Animals ; Antibodies, Viral ; Dengue ; Dengue Virus/physiology ; Furin/genetics ; Mammals ; Serogroup ; Viral Envelope Proteins/genetics ; Virion
Chemical Substances	Antibodies, Viral ; Viral Envelope Proteins ; Furin (EC 3.4.21.75)
Language	English
Publishing date	2022-04-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00386-22
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Article ; Online: SARS-CoV-2 mRNA vaccine induces robust specific and cross-reactive IgG and unequal neutralizing antibodies in naive and previously infected people.

Narowski, Tara M / Raphel, Kristin / Adams, Lily E / Huang, Jenny / Vielot, Nadja A / Jadi, Ramesh / de Silva, Aravinda M / Baric, Ralph S / Lafleur, John E / Premkumar, Lakshmanane

Cell reports

2022 Volume 38, Issue 5, Page(s) 110336

Abstract: Understanding vaccine-mediated protection against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is critical to overcoming the global coronavirus disease 2019 (COVID-19) pandemic. We investigate mRNA-vaccine-induced antibody responses ... ...

Abstract	Understanding vaccine-mediated protection against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is critical to overcoming the global coronavirus disease 2019 (COVID-19) pandemic. We investigate mRNA-vaccine-induced antibody responses against the reference strain, seven variants, and seasonal coronaviruses in 168 healthy individuals at three time points: before vaccination, after the first dose, and after the second dose. Following complete vaccination, both naive and previously infected individuals developed comparably robust SARS-CoV-2 spike antibodies and variable levels of cross-reactive antibodies to seasonal coronaviruses. However, the strength and frequency of SARS-CoV-2 neutralizing antibodies in naive individuals were lower than in previously infected individuals. After the first vaccine dose, one-third of previously infected individuals lacked neutralizing antibodies; this was improved to one-fifth after the second dose. In all individuals, neutralizing antibody responses against the Alpha and Delta variants were weaker than against the reference strain. Our findings support future tailored vaccination strategies against emerging SARS-CoV-2 variants as mRNA-vaccine-induced neutralizing antibodies are highly variable among individuals.
MeSH term(s)	Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; Antibody Formation ; COVID-19/immunology ; COVID-19/prevention & control ; COVID-19 Vaccines/administration & dosage ; COVID-19 Vaccines/immunology ; Coronavirus/immunology ; Cross Reactions ; Humans ; Immunoglobulin G/immunology ; Mutation ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology ; Vaccination ; Vaccines, Synthetic/administration & dosage ; Vaccines, Synthetic/immunology ; mRNA Vaccines/administration & dosage ; mRNA Vaccines/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines ; Immunoglobulin G ; Spike Glycoprotein, Coronavirus ; Vaccines, Synthetic ; mRNA Vaccines
Language	English
Publishing date	2022-01-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.110336
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Article: Comparative Molecular Dynamics Simulations Provide Insight Into Antibiotic Interactions: A Case Study Using the Enzyme L,L-Diaminopimelate Aminotransferase (DapL).

Adams, Lily E / Rynkiewicz, Patrick / Babbitt, Gregory A / Mortensen, Jamie S / North, Rachel A / Dobson, Renwick C J / Hudson, André O

Frontiers in molecular biosciences

2020 Volume 7, Page(s) 46

Abstract: The L,L-diaminopimelate aminotransferase (DapL) pathway, a recently discovered variant of the lysine biosynthetic pathway, is an attractive pipeline to identify targets for the development of novel antibiotic compounds. DapL is a homodimer that catalyzes ...

Abstract	The L,L-diaminopimelate aminotransferase (DapL) pathway, a recently discovered variant of the lysine biosynthetic pathway, is an attractive pipeline to identify targets for the development of novel antibiotic compounds. DapL is a homodimer that catalyzes the conversion of tetrahydrodipicolinate to L,L-diaminopimelate in a single transamination reaction. The penultimate and ultimate products of the lysine biosynthesis pathway,
Language	English
Publishing date	2020-03-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2020.00046
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Article ; Online: DROIDS 1.20: A GUI-Based Pipeline for GPU-Accelerated Comparative Protein Dynamics.

Babbitt, Gregory A / Mortensen, Jamie S / Coppola, Erin E / Adams, Lily E / Liao, Justin K

Biophysical journal

2018 Volume 114, Issue 5, Page(s) 1009–1017

Abstract: Traditional informatics in comparative genomics work only with static representations of biomolecules (i.e., sequence and structure), thereby ignoring the molecular dynamics (MD) of proteins that define function in the cell. A comparative approach ... ...

Abstract	Traditional informatics in comparative genomics work only with static representations of biomolecules (i.e., sequence and structure), thereby ignoring the molecular dynamics (MD) of proteins that define function in the cell. A comparative approach applied to MD would connect this very short timescale process, defined in femtoseconds, to one of the longest in the universe: molecular evolution measured in millions of years. Here, we leverage advances in graphics-processing-unit-accelerated MD simulation software to develop a comparative method of MD analysis and visualization that can be applied to any two homologous Protein Data Bank structures. Our open-source pipeline, DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations), works in conjunction with existing molecular modeling software to convert any Linux gaming personal computer into a "comparative computational microscope" for observing the biophysical effects of mutations and other chemical changes in proteins. DROIDS implements structural alignment and Benjamini-Hochberg-corrected Kolmogorov-Smirnov statistics to compare nanosecond-scale atom bond fluctuations on the protein backbone, color mapping the significant differences identified in protein MD with single-amino-acid resolution. DROIDS is simple to use, incorporating graphical user interface control for Amber16 MD simulations, cpptraj analysis, and the final statistical and visual representations in R graphics and UCSF Chimera. We demonstrate that DROIDS can be utilized to visually investigate molecular evolution and disease-related functional changes in MD due to genetic mutation and epigenetic modification. DROIDS can also be used to potentially investigate binding interactions of pharmaceuticals, toxins, or other biomolecules in a functional evolutionary context as well.
MeSH term(s)	Animals ; Computer Graphics ; Databases, Protein ; Humans ; Molecular Dynamics Simulation ; Protein Conformation ; Proteins/chemistry ; Proteins/metabolism ; Software
Chemical Substances	Proteins
Language	English
Publishing date	2018-03-14
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2018.01.020
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