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Article ; Online: Modelling and Molecular Dynamics Predict the Structure and Interactions of the Glycine Receptor Intracellular Domain.

Thompson, James R E / Beaudoin, Christopher A / Lummis, Sarah C R

2023 Volume 13, Issue 12

Abstract: Glycine receptors (GlyRs) are glycine-gated inhibitory pentameric ligand-gated ion channels composed of α or α + β subunits. A number of structures of these proteins have been reported, but to date, these have only revealed details of the extracellular ... ...

Abstract	Glycine receptors (GlyRs) are glycine-gated inhibitory pentameric ligand-gated ion channels composed of α or α + β subunits. A number of structures of these proteins have been reported, but to date, these have only revealed details of the extracellular and transmembrane domains, with the intracellular domain (ICD) remaining uncharacterised due to its high flexibility. The ICD is a region that can modulate function in addition to being critical for receptor localisation and clustering via proteins such as gephyrin. Here, we use modelling and molecular dynamics (MD) to reveal details of the ICDs of both homomeric and heteromeric GlyR. At their N and C ends, both the α and β subunit ICDs have short helices, which are major sites of stabilising interactions; there is a large flexible loop between them capable of forming transient secondary structures. The α subunit can affect the β subunit ICD structure, which is more flexible in a 4α
MeSH term(s)	Receptors, Glycine/metabolism ; Molecular Dynamics Simulation ; Carrier Proteins/metabolism ; Glycine
Chemical Substances	Receptors, Glycine ; Carrier Proteins ; Glycine (TE7660XO1C)
Language	English
Publishing date	2023-12-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom13121757
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Extensive cellular multi-tasking within

Yannarell, Sarah M / Beaudoin, Eric S / Talley, Hunter S / Schoenborn, Alexi A / Orr, Galya / Anderton, Christopher R / Chrisler, William B / Shank, Elizabeth A

mSystems

2023 Volume 8, Issue 4, Page(s) e0089122

Abstract: ... Bacillus ... ...

Abstract	Bacillus subtilis
MeSH term(s)	Bacillus subtilis/genetics ; Biofilms ; Microscopy, Confocal ; Flow Cytometry ; Cell Differentiation
Language	English
Publishing date	2023-08-01
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.00891-22
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Article ; Online: Can the SARS-CoV-2 Spike Protein Bind Integrins Independent of the RGD Sequence?

Beaudoin, Christopher A / Hamaia, Samir W / Huang, Christopher L-H / Blundell, Tom L / Jackson, Antony P

Frontiers in cellular and infection microbiology

2021 Volume 11, Page(s) 765300

Abstract: The RGD motif in the Severe Acute Syndrome Coronavirus 2 (SARS-CoV-2) spike protein has been predicted to bind RGD-recognizing integrins. Recent studies have shown that the spike protein does, indeed, interact with ... ...

Abstract	The RGD motif in the Severe Acute Syndrome Coronavirus 2 (SARS-CoV-2) spike protein has been predicted to bind RGD-recognizing integrins. Recent studies have shown that the spike protein does, indeed, interact with α
MeSH term(s)	COVID-19 ; Cell Line ; Humans ; Integrins ; Membrane Glycoproteins ; Oligopeptides ; Peptidyl-Dipeptidase A ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; Viral Envelope Proteins
Chemical Substances	Integrins ; Membrane Glycoproteins ; Oligopeptides ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1)
Language	English
Publishing date	2021-11-18
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2021.765300
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Are There Hidden Genes in DNA/RNA Vaccines?

Beaudoin, Christopher A / Bartas, Martin / Volná, Adriana / Pečinka, Petr / Blundell, Tom L

Frontiers in immunology

2022 Volume 13, Page(s) 801915

Abstract: Due to the fast global spreading of the Severe Acute Respiratory Syndrome Coronavirus - 2 (SARS-CoV-2), prevention and treatment options are direly needed in order to control infection-related morbidity, mortality, and economic losses. Although drug and ... ...

Abstract	Due to the fast global spreading of the Severe Acute Respiratory Syndrome Coronavirus - 2 (SARS-CoV-2), prevention and treatment options are direly needed in order to control infection-related morbidity, mortality, and economic losses. Although drug and inactivated and attenuated virus vaccine development can require significant amounts of time and resources, DNA and RNA vaccines offer a quick, simple, and cheap treatment alternative, even when produced on a large scale. The spike protein, which has been shown as the most antigenic SARS-CoV-2 protein, has been widely selected as the target of choice for DNA/RNA vaccines. Vaccination campaigns have reported high vaccination rates and protection, but numerous unintended effects, ranging from muscle pain to death, have led to concerns about the safety of RNA/DNA vaccines. In parallel to these studies, several open reading frames (ORFs) have been found to be overlapping SARS-CoV-2 accessory genes, two of which, ORF2b and ORF-Sh, overlap the spike protein sequence. Thus, the presence of these, and potentially other ORFs on SARS-CoV-2 DNA/RNA vaccines, could lead to the translation of undesired proteins during vaccination. Herein, we discuss the translation of overlapping genes in connection with DNA/RNA vaccines. Two mRNA vaccine spike protein sequences, which have been made publicly-available, were compared to the wild-type sequence in order to uncover possible differences in putative overlapping ORFs. Notably, the Moderna mRNA-1273 vaccine sequence is predicted to contain no frameshifted ORFs on the positive sense strand, which highlights the utility of codon optimization in DNA/RNA vaccine design to remove undesired overlapping ORFs. Since little information is available on ORF2b or ORF-Sh, we use structural bioinformatics techniques to investigate the structure-function relationship of these proteins. The presence of putative ORFs on DNA/RNA vaccine candidates implies that overlapping genes may contribute to the translation of smaller peptides, potentially leading to unintended clinical outcomes, and that the protein-coding potential of DNA/RNA vaccines should be rigorously examined prior to administration.
MeSH term(s)	COVID-19 Vaccines/adverse effects ; COVID-19 Vaccines/genetics ; Codon ; Genes, Overlapping ; Genes, Viral ; Humans ; Nucleic Acid Conformation ; Open Reading Frames ; Protein Biosynthesis ; Protein Domains ; RNA, Messenger ; Spike Glycoprotein, Coronavirus/genetics ; Vaccines, DNA/adverse effects ; Vaccines, DNA/genetics ; mRNA Vaccines/adverse effects ; mRNA Vaccines/genetics
Chemical Substances	COVID-19 Vaccines ; Codon ; RNA, Messenger ; Spike Glycoprotein, Coronavirus ; Vaccines, DNA ; mRNA Vaccines ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-02-08
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.801915
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Article ; Online: What About

St John, Julie / Reininger, Belinda / Balcazar, Hector / Valerio-Shewmaker, Melissa A / Beaudoin, Christopher E

Frontiers in public health

2021 Volume 9, Page(s) 689616

Abstract: This study tested whether a cancer education intervention ... ...

Abstract	This study tested whether a cancer education intervention affected
MeSH term(s)	Community Health Workers ; Cross-Sectional Studies ; Female ; Health Education ; Hispanic or Latino ; Humans ; Uterine Cervical Neoplasms
Language	English
Publishing date	2021-09-10
Publishing country	Switzerland
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2021.689616
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Article: Emotions in the time of coronavirus: Antecedents of digital and social media use among Millennials.

Beaudoin, Christopher E / Hong, Traci

Computers in human behavior

2021 Volume 123, Page(s) 106876

Abstract: Increasingly, people are turning to digital and social media to address health threats. While research has commonly investigated the psychosocial antecedents of digital health information seeking behavior (digital HISB) and social media use (SMU), there ... ...

Abstract	Increasingly, people are turning to digital and social media to address health threats. While research has commonly investigated the psychosocial antecedents of digital health information seeking behavior (digital HISB) and social media use (SMU), there has been limited research on the independent effects of emotions and no research on the interactive effects of emotions. In the context of the coronavirus COVID-19 pandemic, this study investigates the affective, personal relevance, and socio-demographic antecedents of digital HISB and SMU, using data from an online survey of U.S. Millennials (N = 1037) in April-May 2020. Linear regression results show the effects of socio-demographic and personal relevance factors. For the independent effects of emotions, fear and sadness were associated with digital HISB; fear, joy, and disgust were associated with high-informational SMU; and joy and disgust were associated with low-informational SMU. Three interactive effects of discrete negative emotions suggest that an increase in one emotion can amplify the effect of another emotion on a measure of digital and social media use. In the fourth interaction of two negative emotions with strong biological regulatory processes, there is evidence that an increase in one emotion can diminish the effect of another emotion. Implications for theory and practice are discussed.
Language	English
Publishing date	2021-05-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	52665-4
ISSN	0747-5632
ISSN	0747-5632
DOI	10.1016/j.chb.2021.106876
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Article ; Online: Predictors of COVID-19 Preventive Perceptions and Behaviors Among Millennials: Two Cross-sectional Survey Studies.

Beaudoin, Christopher E / Hong, Traci

Journal of medical Internet research

2021 Volume 23, Issue 8, Page(s) e30612

Abstract: Background: COVID-19 preventive perceptions and behaviors, especially among US millennials, are an important means by which the pandemic can be slowed and negative health outcomes can be averted.: Objective: This manuscript aims to advance knowledge ... ...

Abstract	Background: COVID-19 preventive perceptions and behaviors, especially among US millennials, are an important means by which the pandemic can be slowed and negative health outcomes can be averted. Objective: This manuscript aims to advance knowledge on COVID-19 preventive perceptions and behaviors and their main predictors, including digital health information-seeking behavior (HISB), political party identification, and COVID-19 testing status. Methods: Two cross-sectional online surveys of US millennials were conducted from April 10 to 14, 2020 (N=274) (ie, Study 1), and from April 27 to May 7, 2020 (N=1037) (ie, Study 2). In the regression models, dependent variables included preventive behaviors (eg, wearing a face mask and social distancing) as well as four preventive perceptions: severity (ie, a person's conception of the seriousness of COVID-19), susceptibility (ie, a person's conception of the likelihood of being infected with COVID-19), self-efficacy (ie, a person's perception that he or she can wear a face mask and perform social distancing to prevent COVID-19 infection), and response efficacy (ie, a person's perception of whether wearing a face mask and social distancing can prevent COVID-19 infection). Key independent variables included digital HISB for self, digital HISB for another person, political party identification, and COVID-19 testing status. Results: Millennials reported lower levels of perceived susceptibility than the other three preventive perceptions (ie, severity, self-efficacy, and response efficacy), as well as fairly high levels of preventive behaviors. Unlike HISB for another person, digital HISB for self was positively associated with preventive perceptions and behaviors. In Study 1, respondents with higher levels of digital HISB for self had significantly higher perceptions of severity (β=.22, P<.001), self-efficacy (β=.15, P=.02), and response efficacy (β=.25, P<.001) as well as, at nearing significance, higher perceptions of susceptibility (β=.11, P=.07). In Study 2, respondents with higher levels of digital HISB for self had significantly higher perceptions of severity (β=.25, P<.001), susceptibility (β=.14, P<.001), and preventive behaviors (β=.24, P<.001). Preventive behaviors did not vary significantly according to political party identification, but preventive perceptions did. In Study 1, respondents who identified as being more Republican had significantly lower perceptions of self-efficacy (β=-.14, P=.02) and response efficacy (β=-.13, P=.03) and, at nearing significance, lower perceptions of severity (β=-.10, P=.08) and susceptibility (β=-.12, P=.06). In Study 2, respondents who identified as being more Republican had significantly lower perceptions of severity (β=-.08, P=.009). There were mixed effects of COVID-19 testing status on preventive perceptions, with respondents who had tested positive for COVID-19 having significantly higher perceptions of susceptibility in Study 1 (β=.17, P=.006) and significantly lower perceptions of severity in Study 2 (β=-.012, P<.001). Conclusions: As the largest and most digitally savvy generation, US millennials saw COVID-19 as a severe threat, but one that they were less susceptible to. For millennials, digital HISB for self, but not for another person, was critical to the development of preventive perceptions and behaviors.
MeSH term(s)	Adult ; COVID-19/prevention & control ; COVID-19 Testing ; Cross-Sectional Studies ; Female ; Health Behavior ; Humans ; Internet ; Male ; Masks ; Perception ; Physical Distancing ; Politics ; SARS-CoV-2 ; Surveys and Questionnaires
Language	English
Publishing date	2021-08-12
Publishing country	Canada
Document type	Journal Article
ZDB-ID	2028830-X
ISSN	1438-8871 ; 1439-4456
ISSN (online)	1438-8871
ISSN	1439-4456
DOI	10.2196/30612
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Article ; Online: SARS-CoV-2 Omicron subvariant spike N405 unlikely to rapidly deamidate.

Beaudoin, Christopher A / Petsolari, Emmanouela / Hamaia, Samir W / Hala, Sharif / Alofi, Fadwa S / Pandurangan, Arun P / Blundell, Tom L / Chaitanya Vedithi, Sundeep / Huang, Christopher L-H / Jackson, Antony P

Biochemical and biophysical research communications

2023 Volume 666, Page(s) 61–67

Abstract: The RGD motif on the SARS-CoV-2 spike protein has been suggested to interact with RGD-binding integrins αVβ3 and α5β1 to enhance viral cell entry and alter downstream signaling cascades. The D405N mutation on the Omicron subvariant spike proteins, ... ...

Abstract	The RGD motif on the SARS-CoV-2 spike protein has been suggested to interact with RGD-binding integrins αVβ3 and α5β1 to enhance viral cell entry and alter downstream signaling cascades. The D405N mutation on the Omicron subvariant spike proteins, resulting in an RGN motif, has recently been shown to inhibit binding to integrin αVβ3. Deamidation of asparagines in protein ligand RGN motifs has been demonstrated to generate RGD and RGisoD motifs that permit binding to RGD-binding integrins. Two asparagines, N481 and N501, on the Wild-type spike receptor-binding domain have been previously shown to have deamidation half-lives of 16.5 and 123 days, respectively, which may occur during the viral life cycle. Deamidation of Omicron subvariant N405 may recover the ability to interact with RGD-binding integrins. Thus, herein, all-atom molecular dynamics simulations of the Wild-type and Omicron subvariant spike protein receptor-binding domains were conducted to investigate the potential for asparagines, the Omicron subvariant N405 in particular, to assume the optimized geometry for deamidation to occur. In summary, the Omicron subvariant N405 was primarily found to be stabilized in a state unfavourable for deamidation after hydrogen bonding with downstream E406. Nevertheless, a small number of RGD or RGisoD motifs on the Omicron subvariant spike proteins may restore the ability to interact with RGD-binding integrins. The simulations also provided structural clarification regarding the deamidation rates of Wild-type N481 and N501 and highlighted the utility of tertiary structure dynamics information in predicting asparagine deamidation. Further work is needed to characterize the effects of deamidation on spike-integrin interactions.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; Asparagine ; Integrin alphaVbeta3
Chemical Substances	spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Asparagine (7006-34-0) ; Integrin alphaVbeta3
Language	English
Publishing date	2023-05-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2023.04.088
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Article ; Online: SARS-CoV-2 Omicron subvariant spike N405 unlikely to rapidly deamidate

Beaudoin, Christopher A. / Petsolari, Emmanouela / Hamaia, Samir W. / Hala, Sharif / Alofi, Fadwa S. / Pandurangan, Arun P. / Blundell, Tom L. / Chaitanya Vedithi, Sundeep / Huang, Christopher L.-H. / Jackson, Antony P.

Biochemical and Biophysical Research Communications. 2023 July, v. 666 p.61-67

2023

Abstract	The RGD motif on the SARS-CoV-2 spike protein has been suggested to interact with RGD-binding integrins αVβ3 and α5β1 to enhance viral cell entry and alter downstream signaling cascades. The D405N mutation on the Omicron subvariant spike proteins, resulting in an RGN motif, has recently been shown to inhibit binding to integrin αVβ3. Deamidation of asparagines in protein ligand RGN motifs has been demonstrated to generate RGD and RGisoD motifs that permit binding to RGD-binding integrins. Two asparagines, N481 and N501, on the Wild-type spike receptor-binding domain have been previously shown to have deamidation half-lives of 16.5 and 123 days, respectively, which may occur during the viral life cycle. Deamidation of Omicron subvariant N405 may recover the ability to interact with RGD-binding integrins. Thus, herein, all-atom molecular dynamics simulations of the Wild-type and Omicron subvariant spike protein receptor-binding domains were conducted to investigate the potential for asparagines, the Omicron subvariant N405 in particular, to assume the optimized geometry for deamidation to occur. In summary, the Omicron subvariant N405 was primarily found to be stabilized in a state unfavourable for deamidation after hydrogen bonding with downstream E406. Nevertheless, a small number of RGD or RGisoD motifs on the Omicron subvariant spike proteins may restore the ability to interact with RGD-binding integrins. The simulations also provided structural clarification regarding the deamidation rates of Wild-type N481 and N501 and highlighted the utility of tertiary structure dynamics information in predicting asparagine deamidation. Further work is needed to characterize the effects of deamidation on spike-integrin interactions.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; asparagine ; deamidation ; geometry ; half life ; hydrogen ; integrins ; ligands ; molecular dynamics ; mutation ; research ; SARS-CoV-2 ; Spike protein ; Omicron BA.2 ; Omicron BA.5 ; RGD motif
Language	English
Dates of publication	2023-07
Size	p. 61-67.
Publishing place	Elsevier Inc.
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	205723-2
ISSN	0006-291X ; 0006-291X
ISSN (online)	0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2023.04.088
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Article: The challenges of treating patients with trigeminal neuralgia.

Owens, Jessica L / Beaudoin, Danielle A / Spencer, Christopher J

General dentistry

2018 Volume 66, Issue 5, Page(s) 20–23

MeSH term(s)	Communication ; Dentist-Patient Relations ; Humans ; Male ; Middle Aged ; Pain Management/methods ; Tooth Extraction ; Toothache/etiology ; Trigeminal Neuralgia/complications ; Trigeminal Neuralgia/diagnosis ; Trigeminal Neuralgia/therapy
Language	English
Publishing date	2018-09-06
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	603650-8
ISSN	0363-6771
ISSN	0363-6771
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