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November 2019

Biophysics and Biophysical Chemistry Archives

1. Lawson MR, Berger JM. Tuning the sequence specificity of a transcription terminator.
Curr Genet. 2019 Feb 9. doi: 10.1007/s00294-019-00939-1. [Epub ahead of print] Review.
Key words: Hexameric helicase; Molecular motors; NusG; Rho; Spt5; Transcription; Translation

2. Matyszewski M, Zheng W, Lueck J, Antiochos B, Egelman EH, Sohn J. Cryo-EM structure of the NLRC4CARD filament provides insights into how symmetric and asymmetric supramolecular structures drive inflammasome assembly. J Biol Chem. 2018 Dec 28;293(52):20240-20248. doi: 10.1074/jbc.RA118.006050. Epub 2018 Nov 1.
Key words: Monte Carlo simulation; NLRC4; biophysics; caspase; cryo-electron microscopy; inflammasome; innate immunity; nod-like receptor (NLR); pyroptosis

3. Miller MS, Maheshwari S, Shi W, Gao Y, Chu N, Soares AS, Cole PA, Amzel LM, Fuchs MR, Jakoncic J, Gabelli SB. Getting the most out of your crystals: data collection at the new high-flux, microfocus MX beamlines at NSLS-II. Molecules. 2019 Jan 30;24(3). pii: E496. doi: 10.3390/molecules24030496.
Key words: CDP-Chase; NSLS-II; PHM; PI3K?, Akt1; microdiffraction; microfocus; multicrystal; nonhomogeneous crystals; vector data collection

4. Nune M, Morgan MT, Connell Z, McCullough L, Jbara M, Sun H, Brik A, Formosa T, Wolberger C. FACT and Ubp10 collaborate to modulate H2B deubiquitination and nucleosome dynamics. Elife. 2019 Jan 25;8. pii: e40988. doi: 10.7554/eLife.40988.
Key words: DNA replication; S. cerevisiae; biochemistry; chemical biology; chromosomes; deubiquitinating enzyme; gene expression; histone chaperone; nucleosome dynamics; transcription; ubiquitin

5. Schlierf M, Wang G, Chen XS, Ha T. Hexameric helicase G40P unwinds DNA in single base pair steps.
Elife. 2019 Jan 28;8. pii: e42001. doi: 10.7554/eLife.42001.
Key words: DnaB; DnaG; G40P; molecular biophysics; none; single-molecule FRET; structural biology

6. Wied TJ, Chin AC, Lau AY. High conformational variability in the GluK2 Kainate receptor ligand-binding domain. Structure. 2019 Jan 2;27(1):189-195.e2. doi: 10.1016/j.str.2018.09.008.
Key words: free energy calculations; glutamate receptors; kainate receptors; ligand binding; molecular dynamics simulations; small-angle X-ray scattering

7. Worden EJ, Hoffmann NA, Hicks CW, Wolberger C. Mechanism of cross-talk between H2B ubiquitination and H3 methylation by Dot1L. Cell. 2019 Feb 8. pii: S0092-8674(19)30151-5. doi: 10.1016/j.cell.2019.02.002. [Epub ahead of print]
Key words: Dot1L; chromatin; cryo-EM; histones; methylation; nucleosome; structural biology; ubiquitin

1. Yu A, Lau A. Glutamate and glycine binding to the NMDA receptor. Structure. 2018 Jul 3;26(7):1035-1043.e2.
Key words: NMDA receptors; free energy calculations; glutamate receptors; ligand binding; molecular dynamic simulations

1. Parker MW, Botchan MR, Berger JM. Mechanisms and regulation of DNA replication initiation in eukaryotes. Crit Rev Biochem Mol Biol. 2017 Apr;52(2):107-144.
Key words: DNA replication, Helicase, Loader, AAA+, ATPase, CMG; Cdc6; Cdt1; DNA replication; MCM2-7; ORC; helicase; initiator

1. Harden BJ, Frueh DP. Molecular cross-talk between nonribosomal peptide synthetase carrier proteins and unstructured linker regions. Chembiochem. 2017 Jan 24. doi: 10.1002/cbic.201700030.
Key words: allostery; nonribosomal peptide synthetase; nuclear magnetic resonance; protein dynamics; protein folding

1. Thomsen ND, Lawson MR, Witkowsky LB, Qu S, Berger JM. Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7691-E7700.
Key words: Transcription, Helicase, ATPase, Motor Protein, translocase

2. Lawson MR, Dyer K, Berger JM. Ligand-induced and small-molecule control of substrate loading in a hexameric helicase. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):13714-13719.
Key words: Transcription, Helicase, ATPase, Drug Discovery, Motor Protein

1. Yu A, Alberstein R, Thomas A, Zimmet A, Grey R, Mayer ML, Lau AY. Molecular lock regulates binding of glycine to a primitive NMDA receptor. Proc Natl Acad Sci USA. 2016 Nov 1;113(44):E6786-E6795.
Key words: X-ray crystallography; electrophysiology; free energy calculations; glutamate receptors; molecular dynamics simulations

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November 2019 articles:
Changes in HSR Recertification
Research Billing Buzz eNewsletter - November 2019
Update on Insurance and Research Participant Financial Responsibility Information Sheet: Signature No Longer Required
Change in JHM IRB Review Fees for Commercially-Funded Studies
Data and Safety Monitoring Board Training Manual Now Available
Good Clinical Practice (GCP) Fundamentals: Understanding and Applying GCP to Human Subject Research
Fee Schedule Adjustment for Hospital Services Charged to Clinical Trial Budgets
Changes to NIH-funded Human Subjects Research
Free Resources for Longitudinal Clinical Research Studies
JHM IRB Reliance Requests
Sharing Partnership for Innovative Research in Translation
Johns Hopkins Institute for Clinical and Translational Research
Johns Hopkins Clinical Research Network
Visit Animal Care and Use Committee Website
Current Classes
"Interinstitutional Assurance" Agreement
Health, Safety, and Environment (HSE) presents: Safety in Research Updates
Point of Contact for NIH Loan Repayment Program
Michael J. Fox Foundation (MJFF) Challenge
Point of Contact for NIH Loan Repayment Program
JHU SOM Update on NIH Policy on Foreign Involvement
Disclosure of Payments from Foreign Educational Institutions and Government Agencies
Institutional Letter of Support Required for Institutional Training Grant Applications
Notice to the Johns Hopkins Community Regarding the National Science Foundation Grant Reporting Requirement for Harassment Findings and Actions
Prohibited Mention of Prior Review for New Replacement Applications
NIH Policy on Foreign Component Involvement
Why Project Outcomes Matter in your Interim and Final Research Performance Progress Report (RPPR)
NIH Matchmaker, A Tool For Finding Similar NIH Projects
NIH Video Tutorials on How to Apply for Grants

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