1
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Sementilli A, Rengifo RF, Li W, Stewart AM, Stewart KL, Twahir U, Kim Y, Yue J, Mehta AK, Shearer J, Warncke K, Lynn DG. Engineering Synthetic Electron Transfer Chains from Metallopeptide Membranes. Inorg Chem 2024; 63:2899-2908. [PMID: 38127051 PMCID: PMC10865380 DOI: 10.1021/acs.inorgchem.3c02861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
The energetic and geometric features enabling redox chemistry across the copper cupredoxin fold contain key components of electron transfer chains (ETC), which have been extended here by templating the cross-β bilayer assembly of a synthetic nonapeptide, HHQALVFFA-NH2 (K16A), with copper ions. Similar to ETC cupredoxin plastocyanin, these assemblies contain copper sites with blue-shifted (λmax 573 nm) electronic transitions and strongly oxidizing reduction potentials. Electron spin echo envelope modulation and X-ray absorption spectroscopies define square planar Cu(II) sites containing a single His ligand. Restrained molecular dynamics of the cross-β peptide bilayer architecture support metal ion coordination stabilizing the leaflet interface and indicate that the relatively high reduction potential is not simply the result of distorted coordination geometry (entasis). Cyclic voltammetry (CV) supports a charge-hopping mechanism across multiple copper centers placed 10-12 Å apart within the assembled peptide leaflet interface. This metal-templated scaffold accordingly captures the electron shuttle and cupredoxin functionality in a peptide membrane-localized electron transport chain.
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Affiliation(s)
- Anthony Sementilli
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Rolando F. Rengifo
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Wei Li
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Andrew M. Stewart
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Katie L. Stewart
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Umar Twahir
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Youngsun Kim
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Jipeng Yue
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Jason Shearer
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Kurt Warncke
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - David G. Lynn
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
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2
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Klawa SJ, Lee M, Riker KD, Jian T, Wang Q, Gao Y, Daly ML, Bhonge S, Childers WS, Omosun TO, Mehta AK, Lynn DG, Freeman R. Uncovering supramolecular chirality codes for the design of tunable biomaterials. Nat Commun 2024; 15:788. [PMID: 38278785 PMCID: PMC10817930 DOI: 10.1038/s41467-024-45019-2] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/12/2024] [Indexed: 01/28/2024] Open
Abstract
In neurodegenerative diseases, polymorphism and supramolecular assembly of β-sheet amyloids are implicated in many different etiologies and may adopt either a left- or right-handed supramolecular chirality. Yet, the underlying principles of how sequence regulates supramolecular chirality remains unknown. Here, we characterize the sequence specificity of the central core of amyloid-β 42 and design derivatives which enable chirality inversion at biologically relevant temperatures. We further find that C-terminal modifications can tune the energy barrier of a left-to-right chiral inversion. Leveraging this design principle, we demonstrate how temperature-triggered chiral inversion of peptides hosting therapeutic payloads modulates the dosed release of an anticancer drug. These results suggest a generalizable approach for fine-tuning supramolecular chirality that can be applied in developing treatments to regulate amyloid morphology in neurodegeneration as well as in other disease states.
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Affiliation(s)
- Stephen J Klawa
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Michelle Lee
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Kyle D Riker
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Tengyue Jian
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Broad Pharm, San Diego, California, 92121, USA
| | - Qunzhao Wang
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yuan Gao
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Margaret L Daly
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Shreeya Bhonge
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - W Seth Childers
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tolulope O Omosun
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- U.S. Department of Justice, Chicago, IL, 60603, USA
| | - Anil K Mehta
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- The National High Magnetic Field Laboratory, University of Florida, Gainesville, FL, 32611, USA
| | - David G Lynn
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA.
- Department of Biology, Emory University, Atlanta, GA, 30322, USA.
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA.
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3
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Sadihov-Hanoch H, Bandela AK, Chotera-Ouda A, Ben David O, Cohen-Luria R, Lynn DG, Ashkenasy G. Dynamic exchange controls the assembly structure of nucleic-acid-peptide chimeras. Soft Matter 2023; 19:3940-3945. [PMID: 37211859 DOI: 10.1039/d2sm01528e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Recent attempts to develop the next generation of functional biomaterials focus on systems chemistry approaches exploiting dynamic networks of hybrid molecules. This task is often found challenging, but we herein present ways for profiting from the multiple interaction interfaces forming Nucleic-acid-Peptide assemblies and tuning their formation. We demonstrate that the formation of well-defined structures by double-stranded DNA-peptide conjugates (dsCon) is restricted to a specific range of environmental conditions and that precise DNA hybridization, satisfying the interaction interfaces, is a crucial factor in this process. We further reveal the impact of external stimuli, such as competing free DNA elements or salt additives, which initiate dynamic interconversions, resulting in hybrid structures exhibiting spherical and fibrillar domains or a mixture of spherical and fibrillar particles. This extensive analysis of the co-assembly systems chemistry offers new insights into prebiotic hybrid assemblies that may now facilitate the design of new functional materials. We discuss the implications of these findings for the emergence of function in synthetic materials and during early chemical evolution.
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Affiliation(s)
- Hava Sadihov-Hanoch
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Anil Kumar Bandela
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Agata Chotera-Ouda
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Oshrat Ben David
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - David G Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, USA
| | - Gonen Ashkenasy
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
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4
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Gordon-Kim C, Rha A, Poppitz GA, Smith-Carpenter J, Luu R, Roberson AB, Conklin R, Blake A, Lynn DG. Polyanion order controls liquid-to-solid phase transition in peptide/nucleic acid co-assembly. Front Mol Biosci 2022; 9:991728. [PMID: 36452451 PMCID: PMC9702359 DOI: 10.3389/fmolb.2022.991728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/25/2022] [Indexed: 01/06/2024] Open
Abstract
The Central Dogma highlights the mutualistic functions of protein and nucleic acid biopolymers, and this synergy appears prominently in the membraneless organelles widely distributed throughout prokaryotic and eukaryotic organisms alike. Ribonucleoprotein granules (RNPs), which are complex coacervates of RNA with proteins, are a prime example of these membranelles organelles and underly multiple essential cellular functions. Inspired by the highly dynamic character of these organelles and the recent studies that ATP both inhibits and templates phase separation of the fused in sarcoma (FUS) protein implicated in several neurodegenerative diseases, we explored the RNA templated ordering of a single motif of the Aβ peptide of Alzheimer's disease. We now know that this strong cross-β propensity motif alone assembles through a liquid-like coacervate phase that can be externally templated to form distinct supramolecular assemblies. Now we provide evidence that structured phosphates, ranging from complex structures like double stranded and quadraplex DNA to simple trimetaphosphate, differentially impact the liquid to solid phase transition necessary for paracrystalline assembly. The results from this simple model illustrate the potential of ordered environmental templates in the transition to potentially irreversible pathogenic assemblies and provides insight into the ordering dynamics necessary for creating functional synthetic polymer co-assemblies.
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Affiliation(s)
| | - Allisandra Rha
- Children’s Health of Orange County, Research Institute, Orange, CA, United States
| | - George A. Poppitz
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | | | - Regina Luu
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | | | - Russell Conklin
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | - Alexis Blake
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, GA, United States
- Department of Biology, Emory University, Atlanta, GA, United States
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5
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Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Rivka Cohen‐Luria
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
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6
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Abstract
Progressive solute-rich polymer phase transitions provide pathways for achieving ordered supramolecular assemblies. Intrinsically disordered protein domains specifically regulate information in biological networks via conformational ordering. Here we consider a molecular tagging strategy to control ordering transitions in polymeric materials and provide a proof-of-principle minimal peptide phase network captured with a dynamic chemical network. Substrate initiated assembly of a dynamic chemical network.![]()
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Affiliation(s)
- Junjun Tan
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Li Zhang
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Ming-Chien Hsieh
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA .,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta Georgia 30332 USA
| | - Jay T Goodwin
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Martha A Grover
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta Georgia 30332 USA
| | - David G Lynn
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
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7
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Rengifo RF, Sementilli A, Kim Y, Liang C, Li NX, Mehta AK, Lynn DG. Front Cover: Liquid‐Like Phases Preorder Peptides for Supramolecular Assembly (ChemSystemsChem 6/2020). ChemSystemsChem 2020. [DOI: 10.1002/syst.202000047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rolando F. Rengifo
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Anthony Sementilli
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Youngsun Kim
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Chen Liang
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Noel Xiang'An Li
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Anil K. Mehta
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - David G. Lynn
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
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8
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Rengifo RF, Sementilli A, Kim Y, Liang C, Xiang'An Li N, Mehta AK, Lynn DG. Liquid‐Like Phases Preorder Peptides for Supramolecular Assembly. ChemSystemsChem 2020. [DOI: 10.1002/syst.202000046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Rolando F. Rengifo
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322 USA
| | - Anthony Sementilli
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322 USA
| | - Youngsun Kim
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322 USA
| | - Chen Liang
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322 USA
| | - Noel Xiang'An Li
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322 USA
| | - Anil K. Mehta
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322 USA
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9
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10
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Liu S, Lin YH, Murphy A, Anderson J, Walker N, Lynn DG, Binns AN, Pierce BD. Mapping Reaction-Diffusion Networks at the Plant Wound Site With Pathogens. Front Plant Sci 2020; 11:1074. [PMID: 32765558 PMCID: PMC7379035 DOI: 10.3389/fpls.2020.01074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
The rich collection of microbes colonizing the plant root making up the rhizosphere function as a multigenomic organ for nutrient distribution. The extent to which its dynamic mutualistic cellular order depends on morphogenic signaling, while likely, remains unknown. We have shown that reaction-diffusion chemical networks constructed with model plant and bacterial metabolites can mimic processes ranging from oxidative burst kinetics to traveling waves and extracellular stationary state reaction-diffusion networks for spatiotemporal ordering of the rhizosphere. Plant parasites and pathogens can be limited by host attachment require dynamic informational networks and continue to provide insight into what controls the rhizosphere. Here we take advantage of Agrobacterium tumefaciens, a plant pathogen with a gated receptor that requires simultaneous perception of two plant metabolites. Genetic manipulations have created receptors allowing each metabolite concentration to be correlated with pathogen behavior. The development of the florescent strains used here provide initial maps of the reaction-diffusion dynamics existing in the rhizosphere, revealing significant differences in the signaling landscape of host and non-host plants before and after wounding, specifically highlighting networks that may inform rhizosphere organization.
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Affiliation(s)
- Stephanie Liu
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, United States
| | - Yi-Han Lin
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, United States
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, MD, United States
| | - Aidan Murphy
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Josh Anderson
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Nicole Walker
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - David G. Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, United States
| | - Andrew N. Binns
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - B. Daniel Pierce
- Department of Biology, University of Richmond, Richmond, VA, United States
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11
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Affiliation(s)
- Rolando F. Rengifo
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Anthony Sementilli
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Youngsun Kim
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Chen Liang
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Noel Xiang'An Li
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Anil K. Mehta
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - David G. Lynn
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
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12
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Affiliation(s)
- Allisandra K. Rha
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Dibyendu Das
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Olga Taran
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Yonggang Ke
- Biomedical Engineering Emory and Georgia Institute of Technology Atlanta GA 30322 USA
| | - Anil K. Mehta
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
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13
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Rha AK, Das D, Taran O, Ke Y, Mehta AK, Lynn DG. Electrostatic Complementarity Drives Amyloid/Nucleic Acid Co-Assembly. Angew Chem Int Ed Engl 2019; 59:358-363. [PMID: 31617300 DOI: 10.1002/anie.201907661] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/11/2019] [Indexed: 12/20/2022]
Abstract
Proteinaceous plaques associated with neurodegenerative diseases contain many biopolymers including the polyanions glycosaminoglycans and nucleic acids. Polyanion-induced amyloid fibrillation has been implicated in disease etiology, but structural models for amyloid/nucleic acid co-assemblies remain limited. Here we constrain nucleic acid/peptide interactions with model peptides that exploit electrostatic complementarity and define a novel amyloid/nucleic acid co-assembly. The structure provides a model for nucleic acid/amyloid co-assembly as well as insight into the energetic determinants involved in templating amyloid assembly.
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Affiliation(s)
- Allisandra K Rha
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - Dibyendu Das
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - Olga Taran
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - Yonggang Ke
- Biomedical Engineering, Emory and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Anil K Mehta
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - David G Lynn
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
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14
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Grover MA, Hsieh MC, Lynn DG. Systems Analysis for Peptide Systems Chemistry. Life (Basel) 2019; 9:life9030055. [PMID: 31266164 PMCID: PMC6789875 DOI: 10.3390/life9030055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/14/2019] [Accepted: 06/25/2019] [Indexed: 12/21/2022] Open
Abstract
Living systems employ both covalent chemistry and physical assembly to achieve complex behaviors. The emerging field of systems chemistry, inspired by these biological systems, attempts to construct and analyze systems that are simpler than biology, while still embodying biological design principles. Due to the multiple phenomena at play, it can be difficult to predict which phenomena will dominate and when. Conversely, there may be no single rate-limiting step, but rather a reaction network that is difficult to intuit from a purely experimental approach. Mathematical modeling can help to sort out these issues, although it can be challenging to build such models, especially for assembly kinetics. Numerical and statistical methods can play an important role to facilitate the synergistic and iterative use of modeling and experiment, and should be part of a systems chemistry curriculum. Three case studies are presented here, from our work in peptide-based systems, to illustrate some of the tools available for model construction, model simulation, and experimental design. Examples are provided in which these tools help to evaluate hypotheses, uncover design principles, and design new experiments.
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Affiliation(s)
- Martha A Grover
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - David G Lynn
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA.
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15
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Abstract
Molecules released by plants and bacteria form complex abiotic reaction diffusion networks that might regulate the ROS dynamics along the roots of the plants.
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Affiliation(s)
- Olga Taran
- Departments of Chemistry and Biology
- Emory University
- USA
| | - Vraj Patel
- Departments of Chemistry and Biology
- Emory University
- USA
| | - David G. Lynn
- Departments of Chemistry and Biology
- Emory University
- USA
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16
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Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018; 118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.
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Affiliation(s)
- Corey J. Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anant K. Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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17
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Abstract
The recent Research Framework proposed by the US National Institute on Aging and the Alzheimer's Association (NIA-AA) recommends that Alzheimer's disease be defined by its specific biology rather than by non-specific neurodegenerative and syndromal features. By affirming markers of abnormal Aβ and tau proteins as the essential pathobiological signature of Alzheimer's disease, the Framework tacitly reinforces the amyloid (Aβ) cascade as the leading theory of Alzheimer pathogenesis. In light of recent evidence that the cascade is driven by the misfolding and templated aggregation of Aβ and tau, we believe that an empirically grounded Standard Model of Alzheimer's pathogenesis is within reach. A Standard Model can clarify and consolidate existing information, contextualize risk factors and the complex disease phenotype, identify testable hypotheses for future research, and pave the most direct path to effective prevention and treatment.
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Affiliation(s)
- Lary C Walker
- a Department of Neurology and Yerkes National Primate Research Center , Emory University , Atlanta , GA , USA
| | - David G Lynn
- b Departments of Biology and Chemistry , Emory University , Atlanta , GA , USA
| | - Yury O Chernoff
- c School of Biological Sciences , Georgia Institute of Technology , Atlanta , GA , USA.,d Laboratory of Amyloid Biology and Institute of Translational Biomedicine , St. Petersburg State University , St. Petersburg , Russia
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18
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Abstract
Synthetic and materials chemistry initiatives have enabled the translation of the macromolecular functions of biology into synthetic frameworks. These explorations into alternative chemistries of life attempt to capture the versatile functionality and adaptability of biopolymers in new orthogonal scaffolds. Information storage and transfer, however, so beautifully represented in the central dogma of biology, require multiple components functioning synergistically. Over a single decade, the emerging field of systems chemistry has begun to catalyze the construction of mutualistic biopolymer networks, and this review begins with the foundational small-molecule-based dynamic chemical networks and peptide amyloid-based dynamic physical networks on which this effort builds. The approach both contextualizes the versatile approaches that have been developed to enrich chemical information in synthetic networks and highlights the properties of amyloids as potential alternative genetic elements. The successful integration of both chemical and physical networks through β-sheet assisted replication processes further informs the synergistic potential of these networks. Inspired by the cooperative synergies of nucleic acids and proteins in biology, synthetic nucleic-acid-peptide chimeras are now being explored to extend their informational content. With our growing range of synthetic capabilities, structural analyses, and simulation technologies, this foundation is radically extending the structural space that might cross the Darwinian threshold for the origins of life as well as creating an array of alternative systems capable of achieving the progressive growth of novel informational materials.
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Affiliation(s)
- Yushi Bai
- Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, USA.
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19
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Liang C, Hsieh MC, Li NX, Lynn DG. Conformational evolution of polymorphic amyloid assemblies. Curr Opin Struct Biol 2018; 51:135-140. [DOI: 10.1016/j.sbi.2018.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 10/17/2022]
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20
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Abstract
Correction for 'Achieving biopolymer synergy in systems chemistry' by Yushi Bai et al., Chem. Soc. Rev., 2018, DOI: 10.1039/c8cs00174j.
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Affiliation(s)
- Yushi Bai
- Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, USA.
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21
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Taran O, Chen C, Omosun TO, Hsieh MC, Rha A, Goodwin JT, Mehta AK, Grover MA, Lynn DG. Expanding the informational chemistries of life: peptide/RNA networks. Philos Trans A Math Phys Eng Sci 2017; 375:rsta.2016.0356. [PMID: 29133453 DOI: 10.1098/rsta.2016.0356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
- Olga Taran
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Chenrui Chen
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Tolulope O Omosun
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Ming-Chien Hsieh
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Allisandra Rha
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Jay T Goodwin
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Anil K Mehta
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Martha A Grover
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - David G Lynn
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
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22
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Abstract
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Defining pathways
for amyloid assembly could impact therapeutic
strategies for as many as 50 disease states. Here we show that amyloid
assembly is subject to different forces regulating nucleation and
propagation steps and provide evidence that the more global β-sheet/β-sheet
facial complementarity is a critical determinant for amyloid nucleation
and structural selection.
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Affiliation(s)
- Ming-Chien Hsieh
- Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Anil K Mehta
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - David G Lynn
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Martha A Grover
- Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332, United States
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23
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Fuller AW, Young P, Pierce BD, Kitson-Finuff J, Jain P, Schneider K, Lazar S, Taran O, Palmer AG, Lynn DG. Redox-mediated quorum sensing in plants. PLoS One 2017; 12:e0182655. [PMID: 28902851 PMCID: PMC5597120 DOI: 10.1371/journal.pone.0182655] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/22/2017] [Indexed: 11/19/2022] Open
Abstract
The rhizosphere, the narrow zone of soil around plant roots, is a complex network of interactions between plants, bacteria, and a variety of other organisms. The absolute dependence on host-derived signals, or xenognosins, to regulate critical developmental checkpoints for host commitment in the obligate parasitic plants provides a window into the rhizosphere's chemical dynamics. These sessile intruders use H2O2 in a process known as semagenesis to chemically modify the mature root surfaces of proximal host plants and generate p-benzoquinones (BQs). The resulting redox-active signaling network regulates the spatial and temporal commitments necessary for host attachment. Recent evidence from non-parasites, including Arabidopsis thaliana, establishes that reactive oxygen species (ROS) production regulates similar redox circuits related to root recognition, broadening xenognosins' role beyond the parasites. Here we compare responses to the xenognosin dimethoxybenzoquinone (DMBQ) between the parasitic plant Striga asiatica and the non-parasitic A. thaliana. Exposure to DMBQ simulates the proximity of a mature root surface, stimulating an increase in cytoplasmic Ca2+ concentration in both plants, but leads to remarkably different phenotypic responses in the parasite and non-parasite. In S. asiatica, DMBQ induces development of the host attachment organ, the haustorium, and decreases ROS production at the root tip, while in A. thaliana, ROS production increases and further growth of the root tip is arrested. Obstruction of Ca2+ channels and the addition of antioxidants both lead to a decrease in the DMBQ response in both parasitic and non-parasitic plants. These results are consistent with Ca2+ regulating the activity of NADPH oxidases, which in turn sustain the autocatalytic production of ROS via an external quinone/hydroquinone redox cycle. Mechanistically, this chemistry is similar to black and white photography with the emerging dynamic reaction-diffusion network laying the foundation for the precise temporal and spatial control underlying rhizosphere architecture.
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Affiliation(s)
- Alexandra W. Fuller
- Departments of Biology and Chemistry, Emory University, Atlanta, GA, United States of America
| | - Phoebe Young
- Departments of Biology and Chemistry, Emory University, Atlanta, GA, United States of America
| | - B. Daniel Pierce
- Departments of Biology and Chemistry, Emory University, Atlanta, GA, United States of America
- Gottwald Science Center, University of Richmond, Richmond, VA, United States of America
| | - Jamie Kitson-Finuff
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States of America
| | - Purvi Jain
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States of America
| | - Karl Schneider
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States of America
| | - Stephen Lazar
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States of America
| | - Olga Taran
- Departments of Biology and Chemistry, Emory University, Atlanta, GA, United States of America
| | - Andrew G. Palmer
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States of America
| | - David G. Lynn
- Departments of Biology and Chemistry, Emory University, Atlanta, GA, United States of America
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24
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Abstract
Living systems contain remarkable functional capability built within sophisticated self-organizing frameworks. Defining the assembly codes that coordinate these systems could greatly extend nanobiotechnology. To that end, we have highlighted the self-assembling architecture of the chlorosome antenna arrays and report the emulation and extension of their features for the development of cell-compatible photoredox materials. We specifically review work on amyloid peptide scaffolds able to (1) organize light-harvesting chromophores, (2) break peptide bilayer symmetry for directional energy and electron transfer, and (3) incorporate redox active metal ions at high density for energy storage.
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Affiliation(s)
- Rolando F Rengifo
- Emory University, Departments of Biology and Chemistry, 1515 Dickey Dr. NE, Atlanta, GA 30322, USA.
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25
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Affiliation(s)
- Ming-Chien Hsieh
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David G. Lynn
- Departments
of Chemistry and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Martha A. Grover
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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26
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Omosun TO, Hsieh MC, Childers WS, Das D, Mehta AK, Anthony NR, Pan T, Grover MA, Berland KM, Lynn DG. Catalytic diversity in self-propagating peptide assemblies. Nat Chem 2017; 9:805-809. [DOI: 10.1038/nchem.2738] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/19/2017] [Indexed: 01/03/2023]
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27
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Affiliation(s)
- Sha Li
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anil K. Mehta
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton N. Sidorov
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Thomas M. Orlando
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhigang Jiang
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Neil R. Anthony
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David G. Lynn
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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28
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Fang F, Lin YH, Pierce BD, Lynn DG. A Rhizobium radiobacter Histidine Kinase Can Employ Both Boolean AND and OR Logic Gates to Initiate Pathogenesis. Chembiochem 2015; 16:2183-90. [PMID: 26310519 DOI: 10.1002/cbic.201500334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Indexed: 11/12/2022]
Abstract
The molecular logic gates that regulate gene circuits are necessarily intricate and highly regulated, particularly in the critical commitments necessary for pathogenesis. We now report simple AND and OR logic gates to be accessible within a single protein receptor. Pathogenesis by the bacterium Rhizobium radiobacter is mediated by a single histidine kinase, VirA, which processes multiple small molecule host signals (phenol and sugar). Mutagenesis analyses converged on a single signal integration node, and finer functional analyses revealed that a single residue could switch VirA from a functional AND logic gate to an OR gate where each of two signals activate independently. Host range preferences among natural strains of R. radiobacter correlate with these gate logic strategies. Although the precise mechanism for the signal integration node requires further analyses, long-range signal transmission through this histidine kinase can now be exploited for synthetic signaling circuits.
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Affiliation(s)
- Fang Fang
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, 30322, USA
| | - Yi-Han Lin
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, 30322, USA
| | - B Daniel Pierce
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, 30322, USA
| | - David G Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, 30322, USA.
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29
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Smith JE, Liang C, Tseng M, Li N, Li S, Mowles AK, Mehta AK, Lynn DG. Defining the Dynamic Conformational Networks of Cross-β Peptide Assembly. Isr J Chem 2015. [DOI: 10.1002/ijch.201500012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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30
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Li S, Mehta AK, Sidorov A, Orlando TM, Lynn DG. Generation of Electrochemical Gradient from Peptide Self-Assembly. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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31
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Smith JE, Mowles AK, Mehta AK, Lynn DG. Looked at life from both sides now. Life (Basel) 2014; 4:887-902. [PMID: 25513758 PMCID: PMC4284472 DOI: 10.3390/life4040887] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/25/2023] Open
Abstract
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers.
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Affiliation(s)
- Jillian E Smith
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Allisandra K Mowles
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Anil K Mehta
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - David G Lynn
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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32
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Affiliation(s)
- Chen Liang
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Rong Ni
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Jillian E. Smith
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - W. Seth Childers
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - David G. Lynn
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
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33
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Goodwin JT, Lynn DG. Editorial: Ganzheitliche Bildung in Zeiten der Spezialisierung und Globalisierung? Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Goodwin JT, Lynn DG. Editorial: Holistic Education in Times of Specialization and Globalization. Angew Chem Int Ed Engl 2014; 53:6832-3. [DOI: 10.1002/anie.201400597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Li S, Sidorov AN, Mehta AK, Bisignano AJ, Das D, Childers WS, Schuler E, Jiang Z, Orlando TM, Berland K, Lynn DG. Neurofibrillar Tangle Surrogates: Histone H1 Binding to Patterned Phosphotyrosine Peptide Nanotubes. Biochemistry 2014; 53:4225-7. [DOI: 10.1021/bi500599a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Sha Li
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Anton N. Sidorov
- School
of Chemistry and Biochemistry, ⊥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anil K. Mehta
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Anthony J. Bisignano
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Dibyendu Das
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - W. Seth Childers
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Erin Schuler
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | | | - Thomas M. Orlando
- School
of Chemistry and Biochemistry, ⊥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Keith Berland
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - David G. Lynn
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
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36
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Anthony NR, Mehta AK, Lynn DG, Berland KM. Mapping amyloid-β(16-22) nucleation pathways using fluorescence lifetime imaging microscopy. Soft Matter 2014; 10:4162-4172. [PMID: 24763698 DOI: 10.1039/c4sm00361f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The cross-β peptide architecture is associated with numerous functional biomaterials and deleterious disease related aggregates. While these diverse and ubiquitous paracrystalline assemblies have been widely studied, a fundamental understanding of the nucleation and aggregation pathways to these structures remains elusive. Here we highlight a novel application of fluorescence lifetime imaging microscopy in characterising the critical stages of peptide aggregation. Using the central nucleating core of the amyloid-β (Aβ), Aβ(16-22), as a model cross-β system, and utilising a small fraction of rhodamine labelled peptide (Rh110-Aβ(17-22)), we map out a folding pathway from monomer to paracrystalline nanotube. Using this intrinsic fluorescence reporter, we demonstrate the effects of interfaces and evaporation on the nucleation of sub-critical concentration solutions, providing access to previously uncharacterised intermediate morphologies. Using fluorescence lifetime we follow the local peptide environment through the stages of nucleation and hydrophobic collapse, ending in a stable final structure. This work provides a metric for future implementations of measuring fluorescence lifetimes of intrinsic fluorescence reporters during the very dynamic processes relating to peptide nucleation and maturation.
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Affiliation(s)
- Neil R Anthony
- Department of Physics, Emory University, Atlanta, GA, USA.
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37
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Lin YH, Pierce BD, Fang F, Wise A, Binns AN, Lynn DG. Role of the VirA histidine autokinase of Agrobacterium tumefaciens in the initial steps of pathogenesis. Front Plant Sci 2014; 5:195. [PMID: 24860585 PMCID: PMC4030172 DOI: 10.3389/fpls.2014.00195] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/23/2014] [Indexed: 05/27/2023]
Abstract
Histidine kinases serve as critical environmental sensing modules, and despite their designation as simple two-component modules, their functional roles are remarkably diverse. In Agrobacterium tumefaciens pathogenesis, VirA serves with VirG as the initiating sensor/transcriptional activator for inter-kingdom gene transfer and transformation of higher plants. Through responses to three separate signal inputs, low pH, sugars, and phenols, A. tumefaciens commits to pathogenesis in virtually all flowering plants. However, how these three signals are integrated to regulate the response and why these signals might be diagnostic for susceptible cells across such a broad host-range remains poorly understood. Using a homology model of the VirA linker region, we provide evidence for coordinated long-range transmission of inputs perceived both outside and inside the cell through the creation of targeted VirA truncations. Further, our evidence is consistent with signal inputs weakening associations between VirA domains to position the active site histidine for phosphate transfer. This mechanism requires long-range regulation of inter-domain stability and the transmission of input signals through a common integrating domain for VirA signal transduction.
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Affiliation(s)
- Yi-Han Lin
- Lynn Lab, Department of Chemistry and Biology, Emory UniversityAtlanta, GA, USA
| | - B. Daniel Pierce
- Lynn Lab, Department of Chemistry and Biology, Emory UniversityAtlanta, GA, USA
| | - Fang Fang
- Lynn Lab, Department of Chemistry and Biology, Emory UniversityAtlanta, GA, USA
| | - Arlene Wise
- Binns Lab, Department of Biology, Plant Sciences Institute, University of PennsylvaniaPhiladelphia, PA, USA
| | - Andrew N. Binns
- Binns Lab, Department of Biology, Plant Sciences Institute, University of PennsylvaniaPhiladelphia, PA, USA
| | - David G. Lynn
- Lynn Lab, Department of Chemistry and Biology, Emory UniversityAtlanta, GA, USA
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38
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Wiener DM, Esquivel-Suarez F, Gibson B, Gray LA, Templer VL, Taylor L, Lynn DG. Biophysics in Order: An Interdisciplinary Approach to Undergraduate Student Engagement in Research. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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39
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Gierasch LM, Lynn DG, Schneider JP. The Sixth Peptide Engineering Meeting PEM6, Emory University Conference Center, Atlanta, Georgia, October 2 to 5, 2012. Biopolymers 2013; 100:vii. [PMID: 24281724 DOI: 10.1002/bip.22427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Mehta AK, Rosen RF, Childers WS, Gehman JD, Walker LC, Lynn DG. Context dependence of protein misfolding and structural strains in neurodegenerative diseases. Biopolymers 2013; 100:722-30. [PMID: 23893572 PMCID: PMC3979318 DOI: 10.1002/bip.22283] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 04/19/2013] [Accepted: 05/07/2013] [Indexed: 01/28/2023]
Abstract
Vast arrays of structural forms are accessible to simple amyloid peptides and environmental conditions can direct assembly into single phases. These insights are now being applied to the aggregation of the Aβ peptide of Alzheimer's disease and the identification of causative phases. We extend use of the imaging agent Pittsburgh compound B to discriminate among Aβ phases and begin to define conditions of relevance to the disease state. Also, we specifically highlight the development of methods for defining the structures of these more complex phases.
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Affiliation(s)
- Anil K. Mehta
- Departments of Chemistry and Biology, Alzheimer’s Disease Research Center, Emory University, Atlanta, Georgia 30322, USA
| | - Rebecca F. Rosen
- Yerkes National Primate Research Center, Center for Neurodegenerative Disease, Emory University, Atlanta, Georgia 30322, USA
| | - W. Seth Childers
- Departments of Chemistry and Biology, Alzheimer’s Disease Research Center, Emory University, Atlanta, Georgia 30322, USA
| | - John D. Gehman
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Vic. 3010, Australia
| | - Lary C. Walker
- Yerkes National Primate Research Center, Center for Neurodegenerative Disease, Emory University, Atlanta, Georgia 30322, USA
- Department of Neurology, Emory University, Atlanta, Georgia 30322, USA
| | - David G. Lynn
- Departments of Chemistry and Biology, Alzheimer’s Disease Research Center, Emory University, Atlanta, Georgia 30322, USA
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41
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Morgan DM, Lynn DG, Lakdawala AS, Snyder JP, Liotta DC. Amyloid Structure: Models and Theoretical Considerations in Fibrous Aggregates. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200200072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Hernández-Guzmán J, Sun L, Mehta AK, Dong J, Lynn DG, Warncke K. Copper(II)-bis-histidine coordination structure in a fibrillar amyloid β-peptide fragment and model complexes revealed by electron spin echo envelope modulation spectroscopy. Chembiochem 2013; 14:1762-71. [PMID: 24014287 PMCID: PMC3864031 DOI: 10.1002/cbic.201300236] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Indexed: 11/09/2022]
Abstract
Truncated and mutated amyloid-β (Aβ) peptides are models for systematic study-in homogeneous preparations-of the molecular origins of metal ion effects on Aβ aggregation rates, types of aggregate structures formed, and cytotoxicity. The 3D geometry of bis-histidine imidazole coordination of Cu(II) in fibrils of the nonapetide acetyl-Aβ(13-21)H14A has been determined by powder (14) N electron spin echo envelope modulation (ESEEM) spectroscopy. The method of simulation of the anisotropic combination modulation is described and benchmarked for a Cu(II) -bis-cis-imidazole complex of known structure. The revealed bis-cis coordination mode, and the mutual orientation of the imidazole rings, for Cu(II) in Ac-Aβ(13-21)H14A fibrils are consistent with the proposed β-sheet structural model and pairwise peptide interaction with Cu(II) , with an alternating [-metal-vacancy-]n pattern, along the N-terminal edge. Metal coordination does not significantly distort the intra-β-strand peptide interactions, which provides a possible explanation for the acceleration of Ac-Aβ(13-21)H14A fibrillization by Cu(II) , through stabilization of the associated state and low-reorganization integration of β-strand peptide pair precursors.
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Affiliation(s)
- Jessica Hernández-Guzmán
- Dr. J. Hernández-Guzmán, Dr. L. Sun, Prof. K. Warncke Department of Physics Emory University Atlanta, Georgia 30322-2430
| | - Li Sun
- Dr. J. Hernández-Guzmán, Dr. L. Sun, Prof. K. Warncke Department of Physics Emory University Atlanta, Georgia 30322-2430
| | - Anil K. Mehta
- Dr. A. K. Mehta, Dr. J. Dong, Prof. D. G. Lynn Department of Chemistry Emory University Atlanta, Georgia 30322-2430
| | - Jijun Dong
- Dr. A. K. Mehta, Dr. J. Dong, Prof. D. G. Lynn Department of Chemistry Emory University Atlanta, Georgia 30322-2430
| | - David G. Lynn
- Dr. A. K. Mehta, Dr. J. Dong, Prof. D. G. Lynn Department of Chemistry Emory University Atlanta, Georgia 30322-2430
| | - Kurt Warncke
- Dr. J. Hernández-Guzmán, Dr. L. Sun, Prof. K. Warncke Department of Physics Emory University Atlanta, Georgia 30322-2430
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Affiliation(s)
- Rong Ni
- Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, and Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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Abstract
Living matter is the most elaborate, elegant, and complex hierarchical material known and is consequently the natural target for an ever-expanding scientific and technological effort to unlock and deconvolute its marvelous forms and functions. Our current understanding suggests that biological materials are derived from a bottom-up process, a spontaneous emergence of molecular networks in the course of chemical evolution. Polymer cooperation, so beautifully manifested in the ribosome, appeared in these dynamic networks, and the special physicochemical properties of the nucleic and amino acid polymers made possible the critical threshold for the emergence of extant cellular life. These properties include the precise and geometrically discrete hydrogen bonding patterns that dominate the complementary interactions of nucleic acid base-pairing that guide replication and ensure replication fidelity. In contrast, complex and highly context-dependent sets of intra- and intermolecular interactions guide protein folding. These diverse interactions allow the more analog environmental chemical potential fluctuations to dictate conformational template-directed propagation. When these two different strategies converged in the remarkable synergistic ribonucleoprotein that is the ribosome, this resulting molecular digital-to-analog converter achieved the capacity for both persistent information storage and adaptive responses to an ever-changing environment. The ancestral chemical networks that preceded the Central Dogma of Earth's biology must reflect the dynamic chemical evolutionary landscapes that allowed for selection, propagation, and diversification and ultimately the demarcation and specialization of function that modern biopolymers manifest. Not only should modern biopolymers contain molecular fossils of this earlier age, but it should be possible to use this information to reinvent these dynamic functional networks. In this Account, we review the first dynamic network created by modification of a nucleic acid backbone and show how it has exploited the digital-like base pairing for reversible polymer construction and information transfer. We further review how these lessons have been extended to the complex folding landscapes of templated peptide assembly. These insights have allowed for the construction of molecular hybrids of each biopolymer class and made possible the reimagining of chemical evolution. Such elaboration of biopolymer chimeras has already led to applications in therapeutics and diagnostics, to the construction of novel nanostructured materials, and toward orthogonal biochemical pathways that expand the evolution of existing biochemical systems. The ability to look beyond the primordial emergence of the ribosome may allow us to better define the origins of chemical evolution, to extend its horizons beyond the biology of today and ask whether evolution is an inherent property of matter unbounded by physical limitations imposed by our planet's diverse environments.
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Affiliation(s)
- Jay T. Goodwin
- Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, Departments of Chemistry and Biology, Emory University, Atlanta, Georgia, United States
| | - Anil K. Mehta
- Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, Departments of Chemistry and Biology, Emory University, Atlanta, Georgia, United States
| | - David G. Lynn
- Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, Departments of Chemistry and Biology, Emory University, Atlanta, Georgia, United States
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Ni R, Childers WS, Hardcastle KI, Mehta AK, Lynn DG. Remodeling Cross-β Nanotube Surfaces with Peptide/Lipid Chimeras. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Engelhart AE, Cafferty BJ, Okafor CD, Chen MC, Williams LD, Lynn DG, Hud NV. Nonenzymatic Ligation of DNA with a Reversible Step and a Final Linkage that Can Be Used in PCR. Chembiochem 2012; 13:1121-4. [DOI: 10.1002/cbic.201200167] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Indexed: 11/10/2022]
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Abstract
Recent evidence suggests that simple peptides can access diverse amphiphilic phases, and that these structures underlie the robust and widely distributed assemblies implicated in nearly 40 protein misfolding diseases. Here we exploit a minimal nucleating core of the Aβ peptide of Alzheimer's disease to map its morphologically accessible phases that include stable intermolecular molten particles, fibers, twisted and helical ribbons, and nanotubes. Analyses with both fluorescence lifetime imaging microscopy (FLIM) and transmission electron microscopy provide evidence for liquid-liquid phase separations, similar to the coexisting dilute and dense protein-rich liquid phases so critical for the liquid-solid transition in protein crystallization. We show that the observed particles are critical for transitions to the more ordered cross-β peptide phases, which are prevalent in all amyloid assemblies, and identify specific conditions that arrest assembly at the phase boundaries. We have identified a size dependence of the particles in order to transition to the para-crystalline phase and a width of the cross-β assemblies that defines the transition between twisted fibers and helically coiled ribbons. These experimental results reveal an interconnected network of increasing molecularly ordered cross-β transitions, greatly extending the initial computational models for cross-β assemblies.
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Affiliation(s)
- W Seth Childers
- Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, Departments of Chemistry and Biology, Atlanta, Georgia 30322, USA
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Anthony NR, Lynn DG, Berland KM. The Role of Interfaces in the Nucleation of Amyloid Nanotubes. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Gierasch LM, Lynn DG, Schneider J. The Sixth Peptide Engineering Meeting PEM6, Emory University Conference Center, Atlanta, Georgia, October 2 to 5, 2012. Biopolymers 2012; 98:iii. [DOI: 10.1002/bip.22021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Anumukonda LN, Young A, Lynn DG, Buckley R, Warrayat A, Graves CL, Bean HD, Hud NV. Adenine Synthesis in a Model Prebiotic Reaction: Connecting Origin of Life Chemistry with Biology. J Chem Educ 2011; 88:1698-1701. [PMID: 22075932 PMCID: PMC3210525 DOI: 10.1021/ed1012074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Many high school laboratory experiments demonstrate concepts related to biological evolution, but few exist that allow students to investigate life's chemical origins. This series of laboratory experiments has been developed to allow students to explore and appreciate the deep connection that exists between prebiotic chemistry, chemical evolution, and contemporary biological systems. In the first experiment of the series, students synthesize adenine, one of the purine nucleobases of DNA and RNA, from plausibly prebiotic precursor molecules. Students compare their product to authentic standards using thin-layer chromatography. The second and third experiments of the series allow students to extract DNA from a familiar organism, the strawberry, and hydrolyze it, releasing adenine, which they can then compare to the previously chemically-synthesized adenine. A fourth, optional experiment is included where the technique of thin-layer chromatography is introduced and chromatographic skills are developed for use in the other three experiments that comprise this series. Concepts relating to organic and analytical chemistry, as well as biochemistry and DNA structure, are incorporated throughout, allowing this series of laboratory experiments to be easily inserted into existing laboratory courses and to reinforce concepts already included in any high school chemistry or biology curriculum.
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Affiliation(s)
- Lakshmi N. Anumukonda
- Riverwood International Charter School, 5900 Heards Drive NW, Sandy Springs, Georgia 30328, United States
| | - Avery Young
- Roswell High School, 11595 King Road, Roswell, Georgia 30075, United States
| | - David G. Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Ragan Buckley
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Amena Warrayat
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Christina L. Graves
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Heather D. Bean
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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