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Millett P, Alexanian T, Brink KR, Carter SR, Diggans J, Palmer MJ, Ritterson R, Sandbrink JB, Wheeler NE. Beyond Biosecurity by Taxonomic Lists: Lessons, Challenges, and Opportunities. Health Secur 2023; 21:521-529. [PMID: 37856148 PMCID: PMC10733751 DOI: 10.1089/hs.2022.0109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Affiliation(s)
- Piers Millett
- Piers Millett, PhD, is Executive Director, International Biosecurity and Biosafety Initiative for Science, Washington, DC
| | - Tessa Alexanian
- Tessa Alexanian is Safety and Security Program Officer, iGEM Foundation, Paris, France
| | - Kathryn R. Brink
- Kathryn R. Brink, PhD, is a Postdoctoral Fellow, Center for International Security and Cooperation, at Stanford University, Stanford, CA
| | - Sarah R. Carter
- Sarah R. Carter, PhD, is Principal, Science Policy Consulting LLC, Arlington, VA
| | - James Diggans
- James Diggans, PhD, is Head of Biosecurity, Twist Bioscience, San Francisco, CA
| | - Megan J. Palmer
- Megan J. Palmer, PhD, is Executive Director of Bio Policy & Leadership Initiatives and an Adjunct Professor, Department of Bioengineering; at Stanford University, Stanford, CA
| | - Ryan Ritterson
- Ryan Ritterson, PhD, is Executive Vice President of Research, Gryphon Scientific LLC, Takoma Park, MD
| | - Jonas B. Sandbrink
- Jonas B. Sandbrink is a Doctoral Researcher, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicole E. Wheeler
- Nicole E. Wheeler, PhD, is a Turing Fellow, Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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Dettmann RA, Ritterson R, Lauer E, Casagrande R. Concepts to Bolster Biorisk Management. Health Secur 2022; 20:376-386. [PMID: 35997589 DOI: 10.1089/hs.2022.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The rapid increase in the power of the life sciences has not been accompanied by a proportionate increase in the sophistication of biorisk management. Through conversations with thought leaders in biosafety and biosecurity, we have identified 19 concepts that are critical for biorisk management to continue to ensure the responsible and safe conduct of the life sciences in the future. Our work is not meant to be a comprehensive list, but rather a collection of topics that we hope will spark dialogue in the policy, research, and biorisk management communities.
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Affiliation(s)
- Robert August Dettmann
- Robert August Dettmann is an Analyst and MPH Student (Johns Hopkins Bloomberg School of Public Health); Gryphon Scientific, Takoma Park, MD
| | - Ryan Ritterson
- Ryan Ritterson, PhD, is Executive Vice President of Research; Gryphon Scientific, Takoma Park, MD
| | - Erin Lauer
- Erin Lauer is a Senior Analyst; Gryphon Scientific, Takoma Park, MD
| | - Rocco Casagrande
- Rocco Casagrande, PhD, is Chair of the Board; Gryphon Scientific, Takoma Park, MD
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Affiliation(s)
- Ryan Ritterson
- Ryan Ritterson, PhD, is Executive Vice President of Research, Gryphon Scientific, LLC, Takoma Park, MD
| | - Linette Kingston
- Linette Kingston is a Research Assistant, Department of Entomology, University of Maryland, College Park, MD. She was previously affiliated with Gryphon Scientific, LLC
| | - Adam E J Fleming
- Adam E. J. Fleming, PhD, is a Senior Analyst, Gryphon Scientific, LLC, Takoma Park, MD
| | - Erin Lauer
- Erin Lauer is a Senior Analyst, Gryphon Scientific, LLC, Takoma Park, MD
| | - Robert A Dettmann
- Robert A. Dettmann is a Research Assistant, Gryphon Scientific, LLC, Takoma Park, MD
| | - Rocco Casagrande
- Rocco Casagrande, PhD, is Chair of the Board, Gryphon Scientific, LLC, Takoma Park, MD
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Glasgow AA, Huang YM, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. Computational design of a modular protein sense-response system. Science 2020; 366:1024-1028. [PMID: 31754004 DOI: 10.1126/science.aax8780] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/07/2019] [Indexed: 12/28/2022]
Abstract
Sensing and responding to signals is a fundamental ability of living systems, but despite substantial progress in the computational design of new protein structures, there is no general approach for engineering arbitrary new protein sensors. Here, we describe a generalizable computational strategy for designing sensor-actuator proteins by building binding sites de novo into heterodimeric protein-protein interfaces and coupling ligand sensing to modular actuation through split reporters. Using this approach, we designed protein sensors that respond to farnesyl pyrophosphate, a metabolic intermediate in the production of valuable compounds. The sensors are functional in vitro and in cells, and the crystal structure of the engineered binding site closely matches the design model. Our computational design strategy opens broad avenues to link biological outputs to new signals.
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Affiliation(s)
- Anum A Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Yao-Ming Huang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Mandell
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Michael Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ryan Ritterson
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Amanda L Loshbaugh
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Jenna Pellegrino
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Cody Krivacic
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Roland A Pache
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kyle A Barlow
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Noah Ollikainen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Deborah Jeon
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA. .,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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Abstract
We used replica exchange molecular dynamics (REMD) simulations to evaluate four different AMBER force fields and three different implicit solvent models. Our aim was to determine if these physics-based models captured the correct secondary structures of two alpha-helical and two beta-peptides: the 14-mer EK helix of Baldwin and co-workers, the C-terminal helix of ribonuclease, the 16-mer C-terminal hairpin of protein G, and the trpzip2 miniprotein. The different models gave different results, but generally we found that AMBER ff96 plus the implicit solvent model of Onufriev, Bashford, and Case gave reasonable structures, and is fairly well-balanced between helix and sheet. We also observed differences in the strength of ion pairing in the solvent models, we but found that the native secondary structures were retained even when salt bridges were prevented in the conformational sampling. Overall, this work indicates that some of these all-atom physics-based force fields may be good starting points for protein folding and protein structure prediction.
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Affiliation(s)
- M Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106-5080, USA.
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