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Bustorff N, Fitter J. Features of Protein Unfolding Transitions and Their Relation to Domain Topology Probed by Single-Molecule FRET. Biomolecules 2023; 13:1280. [PMID: 37759680 PMCID: PMC10526189 DOI: 10.3390/biom13091280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/10/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
A protein fold is defined as a structural arrangement of a secondary structure in a three-dimensional space. It would be interesting to know whether a particular fold can be assigned to certain features of the corresponding folding/unfolding transitions. To understand the underlying principles of the manifold folding transitions in more detail, single-molecule FRET is the method of choice. Taking the two-domain protein phosphoglycerate kinase (PGK) as an example, we investigated denaturant-induced unfolded states of PGK using the above method. For this purpose, different intramolecular distances within the two domains were measured. In addition to the known two-state transition, a transition with a compact folding intermediate was also identified in each of the two domains. Based on the structural homology of the domains (characterized by a Rossmann fold) and the striking similarity in the features of the measured distance changes during unfolding, clear evidence emerged that the underlying domain topology plays an important role in determining the observed structural changes.
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Affiliation(s)
- Nuno Bustorff
- ER-C-3 Structural Biology & IBI-6 Cellular Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany;
| | - Jörg Fitter
- ER-C-3 Structural Biology & IBI-6 Cellular Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany;
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany
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2
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Zamel J, Chen J, Zaer S, Harris PD, Drori P, Lebendiker M, Kalisman N, Dokholyan NV, Lerner E. Structural and dynamic insights into α-synuclein dimer conformations. Structure 2023; 31:411-423.e6. [PMID: 36809765 PMCID: PMC10081966 DOI: 10.1016/j.str.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/22/2023]
Abstract
Parkinson disease is associated with the aggregation of the protein α-synuclein. While α-synuclein can exist in multiple oligomeric states, the dimer has been a subject of extensive debates. Here, using an array of biophysical approaches, we demonstrate that α-synuclein in vitro exhibits primarily a monomer-dimer equilibrium in nanomolar concentrations and up to a few micromolars. We then use spatial information from hetero-isotopic cross-linking mass spectrometry experiments as restrains in discrete molecular dynamics simulations to obtain the ensemble structure of dimeric species. Out of eight structural sub-populations of dimers, we identify one that is compact, stable, abundant, and exhibits partially exposed β-sheet structures. This compact dimer is the only one where the hydroxyls of tyrosine 39 are in proximity that may promote dityrosine covalent linkage upon hydroxyl radicalization, which is implicated in α-synuclein amyloid fibrils. We propose that this α-synuclein dimer features etiological relevance to Parkinson disease.
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Affiliation(s)
- Joanna Zamel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Sofia Zaer
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paul David Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Mario Lebendiker
- Wolfson Centre for Applied Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA; Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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3
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Jacob MH, D’Souza RN, Lazar AI, Nau WM. Diffusion-Enhanced Förster Resonance Energy Transfer in Flexible Peptides: From the Haas-Steinberg Partial Differential Equation to a Closed Analytical Expression. Polymers (Basel) 2023; 15:polym15030705. [PMID: 36772006 PMCID: PMC9919848 DOI: 10.3390/polym15030705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
In the huge field of polymer structure and dynamics, including intrinsically disordered peptides, protein folding, and enzyme activity, many questions remain that cannot be answered by methodology based on artificial intelligence, X-ray, or NMR spectroscopy but maybe by fluorescence spectroscopy. The theory of Förster resonance energy transfer (FRET) describes how an optically excited fluorophore transfers its excitation energy through space to an acceptor moiety-with a rate that depends on the distance between donor and acceptor. When the donor and acceptor moiety are conjugated to different sites of a flexible peptide chain or any other linear polymer, the pair could in principle report on chain structure and dynamics, on the site-to-site distance distribution, and on the diffusion coefficient of mutual site-to-site motion of the peptide chain. However, the dependence of FRET on distance distribution and diffusion is not defined by a closed analytical expression but by a partial differential equation (PDE), by the Haas-Steinberg equation (HSE), which can only be solved by time-consuming numerical methods. As a second complication, time-resolved FRET measurements have thus far been deemed necessary. As a third complication, the evaluation requires a computationally demanding but indispensable global analysis of an extended experimental data set. These requirements have made the method accessible to only a few experts. Here, we show how the Haas-Steinberg equation leads to a closed analytical expression (CAE), the Haas-Steinberg-Jacob equation (HSJE), which relates a diffusion-diagnosing parameter, the effective donor-acceptor distance, to the augmented diffusion coefficient, J, composed of the diffusion coefficient, D, and the photophysical parameters that characterize the used FRET method. The effective donor-acceptor distance is easily retrieved either through time-resolved or steady-state fluorescence measurements. Any global fit can now be performed in seconds and minimizes the sum-of-square difference between the experimental values of the effective distance and the values obtained from the HSJE. In summary, the HSJE can give a decisive advantage in applying the speed and sensitivity of FRET spectroscopy to standing questions of polymer structure and dynamics.
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4
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Yukhnovets O, Höfig H, Bustorff N, Katranidis A, Fitter J. Impact of Molecule Concentration, Diffusion Rates and Surface Passivation on Single-Molecule Fluorescence Studies in Solution. Biomolecules 2022; 12:biom12030468. [PMID: 35327660 PMCID: PMC8946791 DOI: 10.3390/biom12030468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
For single-molecule studies in solution, very small concentrations of dye-labelled molecules are employed in order to achieve single-molecule sensitivity. In typical studies with confocal microscopes, often concentrations in the pico-molar regime are required. For various applications that make use of single-molecule Förster resonance energy transfer (smFRET) or two-color coincidence detection (TCCD), the molecule concentration must be set explicitly to targeted values and furthermore needs to be stable over a period of several hours. As a consequence, specific demands must be imposed on the surface passivation of the cover slides during the measurements. The aim of having only one molecule in the detection volume at the time is not only affected by the absolute molecule concentration, but also by the rate of diffusion. Therefore, we discuss approaches to control and to measure absolute molecule concentrations. Furthermore, we introduce an approach to calculate the probability of chance coincidence events and demonstrate that measurements with challenging smFRET samples require a strict limit of maximal sample concentrations in order to produce meaningful results.
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Affiliation(s)
- Olessya Yukhnovets
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany;
- Correspondence: (O.Y.); (J.F.)
| | - Henning Höfig
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany;
| | - Nuno Bustorff
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3), Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich, 52425 Jülich, Germany; (N.B.); (A.K.)
| | - Alexandros Katranidis
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3), Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich, 52425 Jülich, Germany; (N.B.); (A.K.)
| | - Jörg Fitter
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany;
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3), Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich, 52425 Jülich, Germany; (N.B.); (A.K.)
- Correspondence: (O.Y.); (J.F.)
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Bandyopadhyay D, Mishra PP. Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy. Front Mol Biosci 2021; 8:725541. [PMID: 34540899 PMCID: PMC8446445 DOI: 10.3389/fmolb.2021.725541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.
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Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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Huang Q, Li N, Zhang H, Che C, Sun F, Xiong Y, Canady TD, Cunningham BT. Critical Review: digital resolution biomolecular sensing for diagnostics and life science research. LAB ON A CHIP 2020; 20:2816-2840. [PMID: 32700698 PMCID: PMC7485136 DOI: 10.1039/d0lc00506a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.
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Affiliation(s)
- Qinglan Huang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Hanyuan Zhang
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Congnyu Che
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Fu Sun
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Taylor D. Canady
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Illinois Cancer Center, University of Illinois at Urbana-Champaign Urbana, IL 61801
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8
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Kennedy AD, Pappan KL, Donti T, Delgado MR, Shinawi M, Pearson TS, Lalani SR, Craigen WJ, Sutton VR, Evans AM, Sun Q, Emrick LT, Elsea SH. Corrigendum: 2-Pyrrolidinone and Succinimide as Clinical Screening Biomarkers for GABA-Transaminase Deficiency: Anti-seizure Medications Impact Accurate Diagnosis. Front Neurosci 2020; 13:1344. [PMID: 32082103 PMCID: PMC7001677 DOI: 10.3389/fnins.2019.01344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 11/28/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | - Taraka Donti
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Mauricio R. Delgado
- Department of Neurology and Neurotherapeutics, Texas Scottish Rite Hospital for Children, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Marwan Shinawi
- Department of Pediatrics, Washington University School of Medicine St. Louis, St. Louis, MO, United States
| | - Toni S. Pearson
- Department of Neurology, Washington University School of Medicine St. Louis, St. Louis, MO, United States
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - William J. Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | | | - Qin Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Lisa T. Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Department of Neurology, Baylor College of Medicine, Houston, TX, United States
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- *Correspondence: Sarah H. Elsea ;
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9
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Kennedy AD, Pappan KL, Donti T, Delgado MR, Shinawi M, Pearson TS, Lalani SR, Craigen WE, Sutton VR, Evans AM, Sun Q, Emrick LT, Elsea SH. 2-Pyrrolidinone and Succinimide as Clinical Screening Biomarkers for GABA-Transaminase Deficiency: Anti-seizure Medications Impact Accurate Diagnosis. Front Neurosci 2019; 13:394. [PMID: 31133775 PMCID: PMC6517487 DOI: 10.3389/fnins.2019.00394] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/05/2019] [Indexed: 11/13/2022] Open
Abstract
Broad-scale untargeted biochemical phenotyping is a technology that supplements widely accepted assays, such as organic acid, amino acid, and acylcarnitine analyses typically utilized for the diagnosis of inborn errors of metabolism. In this study, we investigate the analyte changes associated with 4-aminobutyrate aminotransferase (ABAT, GABA transaminase) deficiency and treatments that affect GABA metabolism. GABA-transaminase deficiency is a rare neurodevelopmental and neurometabolic disorder caused by mutations in ABAT and resulting in accumulation of GABA in the cerebrospinal fluid (CSF). For that reason, measurement of GABA in CSF is currently the primary approach to diagnosis. GABA-transaminase deficiency results in severe developmental delay with intellectual disability, seizures, and movement disorder, and is often associated with death in childhood. Using an untargeted metabolomics platform, we analyzed EDTA plasma, urine, and CSF specimens from four individuals with GABA-transaminase deficiency to identify biomarkers by comparing the biochemical profile of individual patient samples to a pediatric-centric population cohort. Metabolomic analyses of over 1,000 clinical plasma samples revealed a rich source of biochemical information. Three out of four patients showed significantly elevated levels of the molecule 2-pyrrolidinone (Z-score ≥2) in plasma, and whole exome sequencing revealed variants of uncertain significance in ABAT. Additionally, these same patients also had elevated levels of succinimide in plasma, urine, and CSF and/or homocarnosine in urine and CSF. In the analysis of clinical EDTA plasma samples, the levels of succinimide and 2-pyrrolidinone showed a high level of correlation (R = 0.73), indicating impairment in GABA metabolism and further supporting the association with GABA-transaminase deficiency and the pathogenicity of the ABAT variants. Further analysis of metabolomic data across our patient population revealed the association of elevated levels of 2-pyrrolidinone with administration of vigabatrin, a commonly used anti-seizure medication and a known inhibitor of GABA-transaminase. These data indicate that anti-seizure medications may alter the biochemical and metabolomic data, potentially impacting the interpretation and diagnosis for the patient. Further, these data demonstrate the power of combining broad scale genotyping and phenotyping technologies to diagnose inherited neurometabolic disorders and support the use of metabolic phenotyping of plasma to screen for GABA-transaminase deficiency.
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Affiliation(s)
| | | | - Taraka Donti
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Mauricio R Delgado
- Department of Neurology and Neurotherapeutics, Texas Scottish Rite Hospital for Children, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Marwan Shinawi
- Department of Pediatrics, Washington University School of Medicine St. Louis, St. Louis, MO, United States
| | - Toni S Pearson
- Department of Neurology, Washington University School of Medicine St. Louis, St. Louis, MO, United States
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - William E Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | | | - Qin Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Lisa T Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Department of Neurology, Baylor College of Medicine, Houston, TX, United States
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
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10
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Single-Molecule Studies on a FRET Biosensor: Lessons from a Comparison of Fluorescent Protein Equipped versus Dye-Labeled Species. Molecules 2018; 23:molecules23123105. [PMID: 30486450 PMCID: PMC6320824 DOI: 10.3390/molecules23123105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 11/16/2022] Open
Abstract
Bacterial periplasmic binding proteins (PBPs) undergo a pronounced ligand-induced conformational change which can be employed to monitor ligand concentrations. The most common strategy to take advantage of this conformational change for a biosensor design is to use a Förster resonance energy transfer (FRET) signal. This can be achieved by attaching either two fluorescent proteins (FPs) or two organic fluorescent dyes of different colors to the PBPs in order to obtain an optical readout signal which is closely related to the ligand concentration. In this study we compare a FP-equipped and a dye-labeled version of the glucose/galactose binding protein MglB at the single-molecule level. The comparison demonstrates that changes in the FRET signal upon glucose binding are more pronounced for the FP-equipped sensor construct as compared to the dye-labeled analog. Moreover, the FP-equipped sensor showed a strong increase of the FRET signal under crowding conditions whereas the dye-labeled sensor was not influenced by crowding. The choice of a labeling scheme should therefore be made depending on the application of a FRET-based sensor.
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11
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Hamadani KM, Howe J, Jensen MK, Wu P, Cate JHD, Marqusee S. An in vitro tag-and-modify protein sample generation method for single-molecule fluorescence resonance energy transfer. J Biol Chem 2017; 292:15636-15648. [PMID: 28754692 DOI: 10.1074/jbc.m117.791723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/25/2017] [Indexed: 11/06/2022] Open
Abstract
Biomolecular systems exhibit many dynamic and biologically relevant properties, such as conformational fluctuations, multistep catalysis, transient interactions, folding, and allosteric structural transitions. These properties are challenging to detect and engineer using standard ensemble-based techniques. To address this drawback, single-molecule methods offer a way to access conformational distributions, transient states, and asynchronous dynamics inaccessible to these standard techniques. Fluorescence-based single-molecule approaches are parallelizable and compatible with multiplexed detection; to date, however, they have remained limited to serial screens of small protein libraries. This stems from the current absence of methods for generating either individual dual-labeled protein samples at high throughputs or protein libraries compatible with multiplexed screening platforms. Here, we demonstrate that by combining purified and reconstituted in vitro translation, quantitative unnatural amino acid incorporation via AUG codon reassignment, and copper-catalyzed azide-alkyne cycloaddition, we can overcome these challenges for target proteins that are, or can be, methionine-depleted. We present an in vitro parallelizable approach that does not require laborious target-specific purification to generate dual-labeled proteins and ribosome-nascent chain libraries suitable for single-molecule FRET-based conformational phenotyping. We demonstrate the power of this approach by tracking the effects of mutations, C-terminal extensions, and ribosomal tethering on the structure and stability of three protein model systems: barnase, spectrin, and T4 lysozyme. Importantly, dual-labeled ribosome-nascent chain libraries enable single-molecule co-localization of genotypes with phenotypes, are well suited for multiplexed single-molecule screening of protein libraries, and should enable the in vitro directed evolution of proteins with designer single-molecule conformational phenotypes of interest.
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Affiliation(s)
- Kambiz M Hamadani
- From the California Institute for Quantitative Biosciences and .,the Department of Chemistry and Biochemistry, California State University, San Marcos, California 92096, and
| | - Jesse Howe
- the Department of Chemistry and Biochemistry, California State University, San Marcos, California 92096, and
| | | | - Peng Wu
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Jamie H D Cate
- From the California Institute for Quantitative Biosciences and .,the Departments of Molecular and Cell Biology and.,Chemistry, University of California, Berkeley, California 94720
| | - Susan Marqusee
- From the California Institute for Quantitative Biosciences and .,the Departments of Molecular and Cell Biology and
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12
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Portal CF, Seifert JM, Buehler C, Meisner-Kober NC, Auer M. Novel 1:1 Labeling and Purification Process for C-Terminal Thioester and Single Cysteine Recombinant Proteins Using Generic Peptidic Toolbox Reagents. Bioconjug Chem 2014; 25:1213-22. [DOI: 10.1021/bc5000059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Christophe F. Portal
- School
of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, The King’s Buildings, CH Waddington Building
3.07, Mayfield Road, Edinburgh EH9 3JD, United Kingdom
| | - Jan-Marcus Seifert
- Innovative
Screening Technologies Unit, Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
- Marinomed Biotechnologie GmbH, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Christof Buehler
- Innovative
Screening Technologies Unit, Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
- Supercomputing Systems AG, Technoparkstrasse
1, 8005 Zürich, Switzerland
| | - Nicole-Claudia Meisner-Kober
- Innovative
Screening Technologies Unit, Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
- Novartis Institutes for BioMedical Research, Novartis Campus Forum 1, 4056 Basel, Switzerland
| | - Manfred Auer
- School
of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, The King’s Buildings, CH Waddington Building
3.07, Mayfield Road, Edinburgh EH9 3JD, United Kingdom
- Innovative
Screening Technologies Unit, Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
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