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Prieto M. On the foundations of fluorescence: The work of Robert W. Cowgill. Arch Biochem Biophys 2022; 726:109270. [PMID: 35561810 DOI: 10.1016/j.abb.2022.109270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/02/2022]
Abstract
This note on the work of Robert W. Cowgill in 1963 (Archives Biochemistry and Biophysics 100, 36-44), addressing the effect of substituents in indole and phenol compounds as models for tryptophan and tyrosine, intends to frame it within the foundations of protein fluorescence and its applications, considering its relevance and impact.
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Affiliation(s)
- Manuel Prieto
- IBB-Institute for Bioengineering and Biosciences, Associate Laboratory I4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal.
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Pulavarti SVSRK, Maguire JB, Yuen S, Harrison JS, Griffin J, Premkumar L, Esposito EA, Makhatadze GI, Garcia AE, Weiss TM, Snell EH, Kuhlman B, Szyperski T. From Protein Design to the Energy Landscape of a Cold Unfolding Protein. J Phys Chem B 2022; 126:1212-1231. [PMID: 35128921 PMCID: PMC9281400 DOI: 10.1021/acs.jpcb.1c10750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein-water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ∼0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.
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Affiliation(s)
- Surya V S R K Pulavarti
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jack B Maguire
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shirley Yuen
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jermel Griffin
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Edward A Esposito
- Malvern Panalytical Inc, Northhampton, Massachsetts 01060, United States
| | - George I Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 08544, United States
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center, Stanford University, Menlo Park, California 94025, United States
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, United States.,Department of Materials Design and Innovation, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas Szyperski
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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Pinheiro S, Curutchet C. Can Förster Theory Describe Stereoselective Energy Transfer Dynamics in a Protein-Ligand Complex? J Phys Chem B 2017; 121:2265-2278. [PMID: 28235382 DOI: 10.1021/acs.jpcb.7b00217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Förster resonance energy transfer (FRET) reactions involving ligands and aromatic amino acids can substantially impact the fluorescence properties of a protein-ligand complex, an impact intimately related to the corresponding binding mode. Structural characterization of such binding events in terms of intermolecular distances can be done through the well-known R-6 distance-dependent Förster rate expression. However, such an interpretation suffers from uncertainties underlying Förster theory in the description of the electronic coupling that promotes FRET, mostly related to the dipole-dipole orientation factor, dielectric screening effects, and deviations from the ideal dipole approximation. Here, we investigate how Förster approximations impact the prediction of energy transfer dynamics in the complex between flurbiprofen (FBP) and human serum albumin (HSA), as well as a model FBP-Trp dyad, in which recent observation of enantioselective fluorescence quenching has been ascribed to energy transfer from FBP to Trp. To this end, we combine classical molecular dynamics simulations with polarizable quantum mechanics/molecular mechanics calculations that allow overcoming Förster approximations. On the basis of our results, we discuss the potential of structure-based simulations in the characterization of drug-binding events through fluorescence techniques. Overall, we find an excellent agreement between theory and experiment both in terms of enantioselectivity and FRET times, thus strongly supporting the reliability of the binding modes proposed for the (S) and (R) enantiomers of FBP. In particular, we show that the dynamic quenching arises from a small fraction of drug bound to the secondary site of HSA at the interface between subdomains IIA and IIB, whereas the enantioselectivity arises from the larger flexibility of the (S)-FBP enantiomer in the binding pocket.
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Affiliation(s)
- Silvana Pinheiro
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona , Av. Joan XXIII s/n, Barcelona 08028, Spain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona , Av. Joan XXIII s/n, Barcelona 08028, Spain
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Zhdanova NG, Maksimov EG, Arutyunyan AM, Fadeev VV, Shirshin EA. Tyrosine fluorescence probing of conformational changes in tryptophan-lacking domain of albumins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:223-229. [PMID: 27918933 DOI: 10.1016/j.saa.2016.11.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/17/2016] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
We addressed the possibility of using tyrosine (Tyr) fluorescence for monitoring conformational changes of proteins which are undetectable via tryptophan (Trp) fluorescence. The model objects, human (HSA) and bovine (BSA) serum albumins, contain one and two Trp residues, respectively, while Tyr is more uniformly distributed over their structure. The results of the investigation of albumins interaction with ethanol using intrinsic Trp and Tyr steady-state and time-resolved picosecond fluorescence indicated the presence of an intermediate at 10% (v/v) of ethanol in solution, that was supported by the results of extrinsic fluorescence measurements with the Nile Red dye. Based on the comparison of HSA and BSA Trp and Tyr fluorescence, it was suggested that conformational changes at low ethanol concentration are located in the domain III of albumins, which lacks tryptophan residues. The sensitivity of Tyr fluorescence to domain III alterations was further verified by studying albumins interaction with GdnHCl.
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Affiliation(s)
- N G Zhdanova
- Department of Physics, M.V. Lomonosov Moscow State University, 119991, Russia.
| | - E G Maksimov
- Department of Biology, M.V. Lomonosov Moscow State University, 119991, Russia
| | - A M Arutyunyan
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991, Russia
| | - V V Fadeev
- Department of Physics, M.V. Lomonosov Moscow State University, 119991, Russia
| | - E A Shirshin
- Department of Physics, M.V. Lomonosov Moscow State University, 119991, Russia.
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