1
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Berger E, Niemelä J, Lampela O, Juffer AH, Komsa HP. Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities. J Chem Inf Model 2024; 64:4601-4612. [PMID: 38829726 DOI: 10.1021/acs.jcim.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can nowadays be efficiently obtained via machine learning models trained on first-principles data. However, the transferability of the models trained on small molecules to larger structures is unclear, and direct training on large structures is prohibitively expensive. In this work, we first train two machine learning models to predict the polarizabilities of all 20 amino acids. Both models are carefully benchmarked and compared to density functional theory (DFT) calculations, with the neural network method being found to offer better transferability. By combination of machine learning models with classical force field molecular dynamics, Raman spectra of all amino acids are also obtained and investigated, showing good agreement with experiments. The models are further extended to small peptides. We find that adding structures containing peptide bonds to the training set greatly improves predictions, even for peptides not included in training sets.
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Affiliation(s)
- Ethan Berger
- Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, P.O. Box 4500, Oulu FIN-90014, Finland
| | - Juha Niemelä
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland
| | - Outi Lampela
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland
| | - André H Juffer
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland
| | - Hannu-Pekka Komsa
- Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, P.O. Box 4500, Oulu FIN-90014, Finland
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2
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Li Z, Hu R, Li T, Zhu J, You H, Li Y, Liu BF, Li C, Li Y, Yang Y. A TeZla micromixer for interrogating the early and broad folding landscape of G-quadruplex via multistage velocity descending. Proc Natl Acad Sci U S A 2024; 121:e2315401121. [PMID: 38232280 PMCID: PMC10823215 DOI: 10.1073/pnas.2315401121] [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: 09/08/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024] Open
Abstract
Biomacromolecular folding kinetics involves fast folding events and broad timescales. Current techniques face limitations in either the required time resolution or the observation window. In this study, we developed the TeZla micromixer, integrating Tesla and Zigzag microstructures with a multistage velocity descending strategy. TeZla achieves a significant short mixing dead time (40 µs) and a wide time window covering four orders of magnitude (up to 300 ms). Using this unique micromixer, we explored the folding landscape of c-Myc G4 and its noncanonical-G4 derivatives with different loop lengths or G-vacancy sites. Our findings revealed that c-Myc can bypass folding intermediates and directly adopt a G4 structure in the cation-deficient buffer. Moreover, we found that the loop length and specific G-vacancy site could affect the folding pathway and significantly slow down the folding rates. These results were also cross-validated with real-time NMR and circular dichroism. In conclusion, TeZla represents a versatile tool for studying biomolecular folding kinetics, and our findings may ultimately contribute to the design of drugs targeting G4 structures.
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Affiliation(s)
- Zheyu Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Tao Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Huijuan You
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics—Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics—Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
- Optics Valley Laboratory, Hubei430074, China
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3
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Chakrabarty S, Ghosh A. Inconsistent hydrogen bond-mediated vibrational coupling of amide I. RSC Adv 2023; 13:1295-1300. [PMID: 36686902 PMCID: PMC9814034 DOI: 10.1039/d2ra07177k] [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] [Received: 11/12/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Using infrared spectroscopy and density functional theory (DFT) calculations, we scrutinized an amide (dimethylformamide) as a "model" compound to interpret the interactions of amide 1 with different phenol derivatives (para-chlorophenol (PCP) and para-cresol (CP)) as "model guest molecules". We established the involvement of amide I in vibrational coupling with symmetric and asymmetric C[double bond, length as m-dash]C modes of different phenolic derivatives and how their coupling was dependent upon different guest aromatic phenolic compounds. Interestingly, substitution of phenol perturbed the pattern of vibrational coupling with amide I. The symmetric and asymmetric C[double bond, length as m-dash]C modes of PC were coupled significantly with amide 1. For PCP, the symmetric C[double bond, length as m-dash]C mode coupled significantly, but the asymmetric mode coupled negligibly, with amide I. Here, we reveal the nature of vibrational coupling based on the structure of a guest molecule hydrogen-bonded with amide I. Our conclusions could be valuable for depiction of the unusual dynamics of coupled amide-I modes as well as the dependency of vibrational coupling on altered factors.
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Affiliation(s)
- Suranjana Chakrabarty
- a, Department of Condensed Matter of Physics and Materials Sciences, S. N. Bose National Centre for Basic SciencesJD Block, Sector-III, Salt Lake CityKolkata – 700 106India
| | - Anup Ghosh
- a, Department of Condensed Matter of Physics and Materials Sciences, S. N. Bose National Centre for Basic SciencesJD Block, Sector-III, Salt Lake CityKolkata – 700 106India
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4
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Politou AS, Pastore A, Temussi PA. An "Onion-like" Model of Protein Unfolding: Collective versus Site Specific Approaches. Chemphyschem 2021; 23:e202100520. [PMID: 34549492 DOI: 10.1002/cphc.202100520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/09/2021] [Indexed: 11/10/2022]
Abstract
Approximating protein unfolding by an all-or-none cooperative event is a convenient assumption that can provide precious global information on protein stability. It is however quickly emerging that the scenario is far more complex and that global denaturation curves often hide a rich heterogeneity of states that are largely probe dependent. In this review, we revisit the importance of gaining site-specific information on the unfolding process. We focus on nuclear magnetic resonance, as this is the main technique able to provide site-specific information. We review historical and most modern approaches that have allowed an appreciable advancement of the field of protein folding. We also demonstrate how unfolding is a reporter dependent event, suggesting the outmost importance of selecting the reporter carefully.
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Affiliation(s)
- Anastasia S Politou
- Faculty of Medicine, University of Ioannina.,Institute of Molecular Biology and Biotechnology-FORTH, Ioannina, Greece
| | - Annalisa Pastore
- UK Dementia Research Institute at the, Maurice Wohl Institute of King's College London, 5 Cutcombe Rd, London, SE5 9RT, United Kingdom
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the, Maurice Wohl Institute of King's College London, 5 Cutcombe Rd, London, SE5 9RT, United Kingdom
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5
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Kuhar N, Sil S, Umapathy S. Potential of Raman spectroscopic techniques to study proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119712. [PMID: 33965670 DOI: 10.1016/j.saa.2021.119712] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/23/2021] [Accepted: 03/12/2021] [Indexed: 05/18/2023]
Abstract
Proteins are large, complex molecules responsible for various biological processes. However, protein misfolding may lead to various life-threatening diseases. Therefore, it is vital to understand the shape and structure of proteins. Despite numerous techniques, a mechanistic understanding of the protein folding process is still unclear. Therefore, new techniques are continually being explored. In the present article, we have discussed the importance of Raman spectroscopy, Raman Optical Activity (ROA) and various other advancements in Raman spectroscopy to understand protein structure and conformational changes based on the review of our earlier work and recent literature. A Raman spectrum of a protein provides unique signatures for various secondary structures like helices, beta-sheets, turns, random structures, etc., and various amino acid residues such as tyrosine, tryptophan, and phenylalanine. We have shown how Raman spectra can differentiate between bovine serum albumin (BSA) and lysozyme protein based on their difference in sequence and structure (primary, secondary and tertiary). Although it is challenging to elucidate the structure of a protein using a Raman spectrum alone, Raman spectra can be used to differentiate small changes in conformations of proteins such as BSA during melting. Various new advancements in technique and data analyses in Raman spectroscopic studies of proteins have been discussed. The last part of the review focuses on the importance of the ROA spectrum to understand additional features about proteins. The ROA spectrum is rich in information about the protein backbone due to its rigidity compared to its side chains. Furthermore, the ROA spectra of lysozyme and BSA have been presented to show how ROA provides extra information about the solvent properties of proteins.
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Affiliation(s)
- Nikki Kuhar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru 560 012, Karnataka, India
| | - Sanchita Sil
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru 560 012, Karnataka, India; Defence Bioengineering and Electromedical Laboratory (DEBEL), Defence Research and Development Organization (DRDO), C V Raman Nagar, Bangalore 560 093, Karnataka, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru 560 012, Karnataka, India; Department of Instrumentation & Applied Physics, Indian Institute of Science, Bengaluru 560 012, Karnataka, India.
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6
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Micikas RJ, Ahmed IA, Acharyya A, Smith AB, Gai F. Tuning the electronic transition energy of indole via substitution: application to identify tryptophan-based chromophores that absorb and emit visible light. Phys Chem Chem Phys 2021; 23:6433-6437. [PMID: 33710175 DOI: 10.1039/d0cp06710e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fluorescent amino acids (FAAs) offer significant advantages over fluorescent proteins in applications where the fluorophore size needs to be limited or minimized. A long-sought goal in biological spectroscopy/microcopy is to develop visible FAAs by modifying the indole ring of tryptophan. Herein, we examine the absorption spectra of a library of 4-substituted indoles and find that the frequency of the absorption maximum correlates linearly with the global electrophilicity index of the substituent. This finding permits us to identify two promising candidates, 4-formyltryptophan (4CHO-Trp) and 4-nitrotryptophan (4NO2-Trp), both of which can be excited by visible light. Further fluorescence measurements indicate that while 4CHO-indole (and 4CHO-Trp) emits cyan fluorescence with a reasonably large quantum yield (ca. 0.22 in ethanol), 4NO2-indole is essentially non-fluorescent, suggesting that 4CHO-Trp (4NO2-Trp) could be useful as a fluorescence reporter (quencher). In addition, we present a simple method for synthesizing 4CHO-Trp.
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Affiliation(s)
- Robert J Micikas
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
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7
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Edington SC, Liu S, Baiz CR. Infrared spectroscopy probes ion binding geometries. Methods Enzymol 2021; 651:157-191. [PMID: 33888203 DOI: 10.1016/bs.mie.2020.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Stephanie Liu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States.
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8
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Park JY, Kwon HJ, Mondal S, Han H, Kwak K, Cho M. Two-dimensional IR spectroscopy reveals a hidden Fermi resonance band in the azido stretch spectrum of β-azidoalanine. Phys Chem Chem Phys 2020; 22:19223-19229. [PMID: 32812969 DOI: 10.1039/d0cp02693j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Azido stretch modes in a variety of azido-derivatized nonnatural amino acids and nucleotides have been used as a site-specific infrared (IR) probe for monitoring changes in their conformations and local electrostatic environments. The vibrational bands of azide probes are often accompanied by complex line shapes with shoulder peaks, which may arise either from incomplete background subtraction, Fermi resonance, or multiple conformers. The isotope substitution in the infrared probe has thus been introduced to remove Fermi resonances without causing a significant perturbation to the structure. Here, we synthesized and labeled the mid-N atoms of aliphatic azide derivatives with 15N to study the effects of isotope labelling on their vibrational properties. The FT-IR spectra of the aliphatic azide with asymmetric lineshape became a single symmetric band upon isotope substitution, which might be an indication of the removal of the hidden Fermi resonance from the system. We also noticed that the 2D-IR spectrum of unlabeled aliphatic azide has cross-peaks, even though it is not apparently identifiable. The 1D slice spectra obtained from the 2D-IR spectra reveal the existence of a hidden Fermi resonance peak. Furthermore, we show that this weak Fermi resonance does not produce discernible oscillatory beating patterns in the IR pump-probe spectrum, which has been used as evidence of the Fermi resonance. Therefore, we confirm that isotope labelling combined with 2D-IR spectroscopy is the most efficient and incisive way to identify the origin of small shoulder peaks in the linear and nonlinear vibrational spectra of various IR probe molecules.
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Affiliation(s)
- Jun Young Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Hyeok-Jun Kwon
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Saptarsi Mondal
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
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9
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Henry L, Panman MR, Isaksson L, Claesson E, Kosheleva I, Henning R, Westenhoff S, Berntsson O. Real-time tracking of protein unfolding with time-resolved x-ray solution scattering. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:054702. [PMID: 32984436 PMCID: PMC7511240 DOI: 10.1063/4.0000013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/17/2020] [Indexed: 05/14/2023]
Abstract
The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.
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Affiliation(s)
- L. Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - M. R. Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - L. Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - E. Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - I. Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - R. Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - S. Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
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10
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Kuhar N, Umapathy S. Probing the Stepwise Unfolding of Bovine Serum Albumin Using 2D Correlation Raman Spectroscopic Analysis. Anal Chem 2020; 92:13509-13517. [DOI: 10.1021/acs.analchem.0c02968] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nikki Kuhar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
- Department of Instrumentation & Applied Physics, Indian Institute of Science, Bangalore 560012, India
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11
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Flanagan JC, Baiz CR. Ultrafast pH-jump two-dimensional infrared spectroscopy. OPTICS LETTERS 2019; 44:4937-4940. [PMID: 31613233 DOI: 10.1364/ol.44.004937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
We present a pH-jump two-dimensional infrared (2D IR) spectrometer to probe pH-dependent conformational changes from nanoseconds to milliseconds. The design incorporates a nanosecond 355 nm source into a pulse-shaper-based 2D IR spectrometer to trigger dissociation of a caged proton prior to probing subsequent conformational changes with femtosecond 2D IR spectroscopy. We observe a blue shift in the amide I mode (C═O stretch) of diglycine induced by protonation of the terminal amine. This method combines the bond-specific structural sensitivity of ultrafast 2D IR with triggered conformational dynamics, providing structural access to multiscale biomolecular transformations such as protein folding.
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12
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Abstract
Despite the key roles of proteins and nucleic acids in biology, understanding their labile structures and hydrogen bond interactions with guest molecules has posed a critical challenge to the scientific community. In this report, I have used dimethylformamide as a model amide to account for amide hydrogen bond interactions of protein. To quantify hydrogen bond conformation and the structural change, I have monitored the amide I infrared (IR) stretching frequencies while varying the pKa of phenol derivatives. For all phenol derivatives, amide I has formed one hydrogen bond and two hydrogen bond conformation. It has been observed that the formation constant for one hydrogen bond is higher than that of two hydrogen bonds for all phenol derivatives. During the formation of hydrogen bond with amide I, IR absorbance of C═C transition is enhanced for all phenol derivatives. Enhancement of the IR absorbance of the C═C transition indicates hydrogen bond-assisted vibrational coupling between the amide I and phenol ring transition. The relative coupling constant is estimated to be higher for single hydrogen-bonded conformer than the double hydrogen-bonded conformer. This is an intriguing result as the frequency difference between the two coupled transitions predicts otherwise. Using IR absorption spectroscopy, a delicate interplay between hydrogen bonding conformations and intermolecular vibrational coupling between amide I and H-bond donor phenol molecules has been shown. This study can be used as a point of reference for understanding the structural information of proteins, peptides, and nucleosides having hydrogen bond interaction with any drug or ligand molecules. My results as well provide an insight into the vibrational coupling of carbonyl and C═C transition of nucleobases.
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Affiliation(s)
- Anup Ghosh
- Department of Condensed Matter Physics and Materials Sciences , S. N. Bose National Centre for Basic Sciences , JD Block, Sector-III, Salt Lake City , Kolkata 700 106 , India
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13
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Application of millisecond time-resolved solid state NMR to the kinetics and mechanism of melittin self-assembly. Proc Natl Acad Sci U S A 2019; 116:16717-16722. [PMID: 31387974 DOI: 10.1073/pnas.1908006116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Common experimental approaches for characterizing structural conversion processes such as protein folding and self-assembly do not report on all aspects of the evolution from an initial state to the final state. Here, we demonstrate an approach that is based on rapid mixing, freeze-trapping, and low-temperature solid-state NMR (ssNMR) with signal enhancements from dynamic nuclear polarization (DNP). Experiments on the folding and tetramerization of the 26-residue peptide melittin following a rapid pH jump show that multiple aspects of molecular structure can be followed with millisecond time resolution, including secondary structure at specific isotopically labeled sites, intramolecular and intermolecular contacts between specific pairs of labeled residues, and overall structural order. DNP-enhanced ssNMR data reveal that conversion of conformationally disordered melittin monomers at low pH to α-helical conformations at neutral pH occurs on nearly the same timescale as formation of antiparallel melittin dimers, about 6 to 9 ms for 0.3 mM melittin at 24 °C in aqueous solution containing 20% (vol/vol) glycerol and 75 mM sodium phosphate. Although stopped-flow fluorescence data suggest that melittin tetramers form quickly after dimerization, ssNMR spectra show that full structural order within melittin tetramers develops more slowly, in ∼60 ms. Time-resolved ssNMR is likely to find many applications to biomolecular structural conversion processes, including early stages of amyloid formation, viral capsid formation, and protein-protein recognition.
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14
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Edington SC, Halling DB, Bennett SM, Middendorf TR, Aldrich RW, Baiz CR. Non-Additive Effects of Binding Site Mutations in Calmodulin. Biochemistry 2019; 58:2730-2739. [PMID: 31124357 DOI: 10.1021/acs.biochem.9b00096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite decades of research on ion-sensing proteins, gaps persist in the understanding of ion binding affinity and selectivity even in well-studied proteins such as calmodulin. Site-directed mutagenesis is a powerful and popular tool for addressing outstanding questions about biological ion binding and is employed to selectively deactivate binding sites and insert chromophores at advantageous positions within ion binding structures. However, even apparently nonperturbative mutations can distort the binding dynamics they are employed to measure. We use Fourier transform infrared (FTIR) and ultrafast two-dimensional infrared (2D IR) spectroscopy of the carboxylate asymmetric stretching mode in calmodulin as a mutation- and label-independent probe of the conformational perturbations induced in calmodulin's binding sites by two classes of mutation, tryptophan insertion and carboxylate side-chain deletion, commonly used to study ion binding in proteins. Our results show that these mutations not only affect ion binding but also induce changes in calmodulin's conformational landscape along coordinates not probed by vibrational spectroscopy, remaining invisible without additional perturbation of binding site structure. Comparison of FTIR line shapes with 2D IR diagonal slices provides a clear example of how nonlinear spectroscopy produces well-resolved line shapes, refining otherwise featureless spectral envelopes into more informative vibrational spectra of proteins.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - D Brent Halling
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Suzanna M Bennett
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Thomas R Middendorf
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Richard W Aldrich
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Carlos R Baiz
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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15
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Mirarefi P, Ted Lee C. Reversible control of enzyme-inhibitor interactions with light illumination using a photoresponsive surfactant. Proteins 2019; 87:715-722. [PMID: 30980557 DOI: 10.1002/prot.25695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 11/07/2022]
Abstract
The effects of a photoresponsive surfactant and light illumination on the complex formed between ribonuclease A (RNase A) and a protein ribonuclease inhibitor (RI) have been investigated to develop a light-based technique to reactivate an enzyme through surfactant-induced dissociation of the enzyme-inhibitor complex. The photoresponsive surfactant undergoes a photoisomerization from the relatively hydrophobic trans isomer under visible light to the relatively hydrophilic cis isomer upon UV illumination, providing a means to reversibly control protein-inhibitor interactions. In the absence of surfactant, RI binds tightly to RNase A through noncovalent interactions, which inhibits the enzyme activity. Upon addition of the surfactant under visible light, RNase A is reactivated, regaining ~75% of the native activity in the absence of RI. In the presence of the surfactant under UV light, however, the enzyme remains inhibited. Fluorescence spectroscopy, dynamic light scattering, and circular dichroism spectroscopy reveal that RI dramatically unfolds upon addition of the trans form of the surfactant, while RNase A does not undergo noticeable structural changes under the same conditions. This indicates that RNase A reactivation occurs through dissociation of the enzyme-inhibitor complex arising from surfactant-induced unfolding of the inhibitor. As a result, photoresponsive surfactant and light illumination can be used as a novel light-based technique to dissociate enzyme-inhibitor complexes and, thus, reactivate an inhibited enzyme.
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Affiliation(s)
- Panteha Mirarefi
- Department of Chemical Engineering and Materials Science, University of Southern California, California, Los Angeles
| | - C Ted Lee
- Department of Chemical Engineering and Materials Science, University of Southern California, California, Los Angeles
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16
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Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane. Biophys J 2019; 116:1692-1700. [PMID: 31000156 DOI: 10.1016/j.bpj.2019.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 01/08/2023] Open
Abstract
Transmembrane peptides contain polar residues in the interior of the membrane, which may alter the electrostatic environment and favor hydration in the otherwise nonpolar environment of the membrane core. Here, we demonstrate a general, nonperturbative strategy to probe hydration of the peptide backbone at specific depths within the bilayer using a combination of site-specific isotope labels, ultrafast two-dimensional infrared spectroscopy, and spectral modeling based on molecular dynamics simulations. Our results show that the amphiphilic pH-low insertion peptide supports a highly heterogeneous environment, with significant backbone hydration of nonpolar residues neighboring charged residues. For example, a leucine residue located as far as 1 nm into the hydrophobic bulk reports hydrogen-bonded populations as high as ∼20%. These findings indicate that the polar nature of these residues may facilitate the transport of water molecules into the hydrophobic core of the membrane.
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17
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Acharyya A, Ge Y, Wu H, DeGrado WF, Voelz VA, Gai F. Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study. J Phys Chem B 2019; 123:1797-1807. [PMID: 30694671 DOI: 10.1021/acs.jpcb.8b12220] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
One of the fundamental events in protein folding is α-helix formation, which involves sequential development of a series of helical hydrogen bonds between the backbone C═O group of residues i and the -NH group of residues i + 4. While we now know a great deal about α-helix folding dynamics, a key question that remains to be answered is where the productive helical nucleation event occurs. Statistically, a helical nucleus (or the first helical hydrogen-bond) can form anywhere within the peptide sequence in question; however, the one that leads to productive folding may only form at a preferred location. This consideration is based on the fact that the α-helical structure is inherently asymmetric, due to the specific alignment of the helical hydrogen bonds. While this hypothesis is plausible, validating it is challenging because there is not an experimental observable that can be used to directly pinpoint the location of the productive nucleation process. Therefore, in this study we combine several techniques, including peptide cross-linking, laser-induced temperature-jump infrared spectroscopy, and molecular dynamics simulations, to tackle this challenge. Taken together, our experimental and simulation results support an α-helix folding mechanism wherein the productive nucleus is formed at the N-terminus, which propagates toward the C-terminal end of the peptide to yield the folded structure. In addition, our results show that incorporation of a cross-linker can lead to formation of differently folded conformations, underscoring the need for all-atom simulations to quantitatively assess the proposed cross-linking design.
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Affiliation(s)
- Arusha Acharyya
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Yunhui Ge
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Haifan Wu
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Vincent A Voelz
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Feng Gai
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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18
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Ahmed IA, Acharyya A, Eng CM, Rodgers JM, DeGrado WF, Jo H, Gai F. 4-Cyanoindole-2'-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics. Molecules 2019; 24:E602. [PMID: 30744004 PMCID: PMC6384856 DOI: 10.3390/molecules24030602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/26/2019] [Accepted: 02/05/2019] [Indexed: 11/16/2022] Open
Abstract
Unnatural nucleosides possessing unique spectroscopic properties that mimic natural nucleobases in both size and chemical structure are ideally suited for spectroscopic measurements of DNA/RNA structure and dynamics in a site-specific manner. However, such unnatural nucleosides are scarce, which prompts us to explore the utility of a recently found unnatural nucleoside, 4-cyanoindole-2'-deoxyribonucleoside (4CNI-NS), as a site-specific spectroscopic probe of DNA. A recent study revealed that 4CNI-NS is a universal nucleobase that maintains the high fluorescence quantum yield of 4-cyanoindole and that among the four natural nucleobases, only guanine can significantly quench its fluorescence. Herein, we further show that the C≡N stretching frequency of 4CNI-NS is sensitive to the local environment, making it a useful site-specific infrared probe of oligonucleotides. In addition, we demonstrate that the fluorescence-quencher pair formed by 4CNI-NS and guanine can be used to quantitatively assess the binding affinity of a single-stranded DNA to the protein system of interest via fluorescence spectroscopy, among other applications. We believe that this fluorescence binding assay is especially useful as its potentiality allows high-throughput screening of DNA⁻protein interactions.
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Affiliation(s)
- Ismail A Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Christina M Eng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jeffrey M Rodgers
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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19
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Feng M, Zhao J, Yu P, Wang J. Linear and Nonlinear Infrared Spectroscopies Reveal Detailed Solute-Solvent Dynamic Interactions of a Nitrosyl Ruthenium Complex in Solution. J Phys Chem B 2018; 122:9225-9235. [PMID: 30200757 DOI: 10.1021/acs.jpcb.8b07247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work, the solvation of a nitrosyl ruthenium complex, [(CH3)4N][RuCl3(qn)(NO)] (with qn = deprotonated 8-hydroxyquinoline), which is a potential NO-releasing molecule in the bio-environment, was studied in two bio-friendly solvents, namely deuterated dimethyl sulfoxide (dDMSO) and water (D2O). A blue-shifted NO stretching frequency was observed in water with respect to that in dDMSO, which was believed to be due to ligand-solvent hydrogen-bonding interactions, one N═O···D and particularly three Ru-Cl···D, that show competing effects on the NO bond length. The dynamic differences of the NO stretch in these two solvents were further revealed by transient pump-probe IR and two-dimensional IR results: faster vibrational relaxation and faster spectral diffusion (SD) were observed in D2O, confirming stronger solvent-solute interaction and also faster solvent structural dynamics in D2O than in DMSO. Further, a significant non-decaying residual in the SD dynamics was observed in D2O but not in DMSO, suggesting the formation of a stable solvation shell in water due to strong multi-site ligand-solvent hydrogen-bonding interactions, which is in agreement with the observed blue-shifted NO stretching frequency. This work demonstrates that small solvent molecules such as water can form a relatively rigid solvation shell for certain transition metal complexes due to cooperative ligand-solvent interactions and show slower dynamics.
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Affiliation(s)
- Minjun Feng
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
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20
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Hogle DG, Cunningham AR, Tucker MJ. Equilibrium versus Nonequilibrium Peptide Dynamics: Insights into Transient 2D IR Spectroscopy. J Phys Chem B 2018; 122:8783-8795. [PMID: 30040900 DOI: 10.1021/acs.jpcb.8b05063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the past two decades, two-dimensional infrared (2D IR) spectroscopy has evolved from the theoretical underpinnings of nonlinear spectroscopy as a means of investigating detailed molecular structure on an ultrafast time scale. The combined time and spectral resolution over which spectra can be collected on complex molecular systems has led to the precise structural resolution of dynamic species that have previously been impossible to directly observe through traditional methods. The adoption of 2D IR spectroscopy for the study of protein folding and peptide interactions has provided key details of how small changes in conformations can exert major influences on the activities of these complex molecular systems. Traditional 2D IR experiments are limited to molecules under equilibrium conditions, where small motions and fluctuations of these larger molecules often still lead to functionality. Utilizing techniques that allow the rapid initiation of chemical or structural changes in conjunction with 2D IR spectroscopy, i.e., transient 2D IR, a vast dynamic range becomes available to the spectroscopist uncovering structural content far from equilibrium. Furthermore, this allows the observation of reaction pathways of these macromolecules under quasi- and nonequilibrium conditions.
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Affiliation(s)
- David G Hogle
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Amy R Cunningham
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Matthew J Tucker
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
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21
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Affiliation(s)
- Sean C. Edington
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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22
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Kinetic and biophysical investigation of the inhibitory effect of caffeine on human salivary aldehyde dehydrogenase: Implications in oral health and chemotherapy. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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Coordination to lanthanide ions distorts binding site conformation in calmodulin. Proc Natl Acad Sci U S A 2018; 115:E3126-E3134. [PMID: 29545272 DOI: 10.1073/pnas.1722042115] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Ca2+-sensing protein calmodulin (CaM) is a popular model of biological ion binding since it is both experimentally tractable and essential to survival in all eukaryotic cells. CaM modulates hundreds of target proteins and is sensitive to complex patterns of Ca2+ exposure, indicating that it functions as a sophisticated dynamic transducer rather than a simple on/off switch. Many details of this transduction function are not well understood. Fourier transform infrared (FTIR) spectroscopy, ultrafast 2D infrared (2D IR) spectroscopy, and electronic structure calculations were used to probe interactions between bound metal ions (Ca2+ and several trivalent lanthanide ions) and the carboxylate groups in CaM's EF-hand ion-coordinating sites. Since Tb3+ is commonly used as a luminescent Ca2+ analog in studies of protein-ion binding, it is important to characterize distinctions between the coordination of Ca2+ and the lanthanides in CaM. Although functional assays indicate that Tb3+ fully activates many Ca2+-dependent proteins, our FTIR spectra indicate that Tb3+, La3+, and Lu3+ disrupt the bidentate coordination geometry characteristic of the CaM binding sites' strongly conserved position 12 glutamate residue. The 2D IR spectra indicate that, relative to the Ca2+-bound form, lanthanide-bound CaM exhibits greater conformational flexibility and larger structural fluctuations within its binding sites. Time-dependent 2D IR lineshapes indicate that binding sites in Ca2+-CaM occupy well-defined configurations, whereas binding sites in lanthanide-bound-CaM are more disordered. Overall, the results show that binding to lanthanide ions significantly alters the conformation and dynamics of CaM's binding sites.
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24
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Hall AR, Geoghegan M. Polymers and biopolymers at interfaces. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:036601. [PMID: 29368695 DOI: 10.1088/1361-6633/aa9e9c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
This review updates recent progress in the understanding of the behaviour of polymers at surfaces and interfaces, highlighting examples in the areas of wetting, dewetting, crystallization, and 'smart' materials. Recent developments in analysis tools have yielded a large increase in the study of biological systems, and some of these will also be discussed, focussing on areas where surfaces are important. These areas include molecular binding events and protein adsorption as well as the mapping of the surfaces of cells. Important techniques commonly used for the analysis of surfaces and interfaces are discussed separately to aid the understanding of their application.
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Affiliation(s)
- A R Hall
- Department of Physics and Astronomy, University of Sheffield, Hounsfield Road, Sheffield S3 7RH, United Kingdom. Fraunhofer Project Centre for Embedded Bioanalytical Systems, Dublin City University, Glasnevin, Dublin 9, Ireland
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25
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Yefremova Y, Danquah BD, Opuni KF, El-Kased R, Koy C, Glocker MO. Mass spectrometric characterization of protein structures and protein complexes in condensed and gas phase. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:445-459. [PMID: 29183193 DOI: 10.1177/1469066717722256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteins are essential for almost all physiological processes of life. They serve a myriad of functions which are as varied as their unique amino acid sequences and their corresponding three-dimensional structures. To fulfill their tasks, most proteins depend on stable physical associations, in the form of protein complexes that evolved between themselves and other proteins. In solution (condensed phase), proteins and/or protein complexes are in constant energy exchange with the surrounding solvent. Albeit methods to describe in-solution thermodynamic properties of proteins and of protein complexes are well established and broadly applied, they do not provide a broad enough access to life-science experimentalists to study all their proteins' properties at leisure. This leaves great desire to add novel methods to the analytical biochemist's toolbox. The development of electrospray ionization created the opportunity to characterize protein higher order structures and protein complexes rather elegantly by simultaneously lessening the need of sophisticated sample preparation steps. Electrospray mass spectrometry enabled us to translate proteins and protein complexes very efficiently into the gas phase under mild conditions, retaining both, intact protein complexes, and gross protein structures upon phase transition. Moreover, in the environment of the mass spectrometer (gas phase, in vacuo), analyte molecules are free of interactions with surrounding solvent molecules and, therefore, the energy of inter- and intramolecular forces can be studied independently from interference of the solvating environment. Provided that gas phase methods can give information which is relevant for understanding in-solution processes, gas phase protein structure studies and/or investigations on the characterization of protein complexes has rapidly gained more and more attention from the bioanalytical scientific community. Recent reports have shown that electrospray mass spectrometry provides direct access to six prime protein complex properties: stabilities, compositions, binding surfaces (epitopes), disassembly processes, stoichiometries, and thermodynamic parameters.
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Affiliation(s)
- Yelena Yefremova
- 1 Proteome Center Rostock, University of Rostock, Rostock, Germany
| | - Bright D Danquah
- 1 Proteome Center Rostock, University of Rostock, Rostock, Germany
| | | | - Reham El-Kased
- 3 Microbiology and Immunology, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cornelia Koy
- 1 Proteome Center Rostock, University of Rostock, Rostock, Germany
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26
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Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation. Sci China Chem 2017. [DOI: 10.1007/s11426-016-9055-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Abaskharon RM, Gai F. Meandering Down the Energy Landscape of Protein Folding: Are We There Yet? Biophys J 2017; 110:1924-32. [PMID: 27166801 DOI: 10.1016/j.bpj.2016.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
As judged by a single publication metric, the activity in the protein folding field has been declining over the past 5 years, after enjoying a decade-long growth. Does this development indicate that the field is sunsetting or is this decline only temporary? Upon surveying a small territory of its landscape, we find that the protein folding field is still quite active and many important findings have emerged from recent experimental studies. However, it is also clear that only continued development of new techniques and methods, especially those enabling dissection of the fine details and features of the protein folding energy landscape, will fuel this old field to move forward.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania; The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania.
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28
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Balobanov VA, Katina NS, Finkelstein AV, Bychkova VE. Intermediate states of apomyoglobin: Are they parts of the same area of conformations diagram? BIOCHEMISTRY (MOSCOW) 2017; 82:625-631. [DOI: 10.1134/s0006297917050108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Davis CM, Reddish MJ, Dyer RB. Dual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 178:185-191. [PMID: 28189834 PMCID: PMC5346054 DOI: 10.1016/j.saa.2017.01.069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/27/2017] [Accepted: 01/31/2017] [Indexed: 05/30/2023]
Abstract
Time-resolved temperature-jump (T-jump) coupled with fluorescence and infrared (IR) spectroscopy is a powerful technique for monitoring protein dynamics. Although IR spectroscopy of the polypeptide amide I mode is more technically challenging, it offers complementary information because it directly probes changes in the protein backbone, whereas, fluorescence spectroscopy is sensitive to the environment of specific side chains. With the advent of widely tunable quantum cascade lasers (QCL) it is possible to efficiently probe multiple IR frequencies with high sensitivity and reproducibility. Here we describe a dual time-resolved T-jump fluorescence and IR spectrometer and its application to study protein folding dynamics. A Q-switched Ho:YAG laser provides the T-jump source for both time-resolved IR and fluorescence spectroscopy, which are probed by a QCL and Ti:Sapphire laser, respectively. The Ho:YAG laser simultaneously pumps the time-resolved IR and fluorescence spectrometers. The instrument has high sensitivity, with an IR absorbance detection limit of <0.2mOD and a fluorescence sensitivity of 2% of the overall fluorescence intensity. Using a computer controlled QCL to rapidly tune the IR frequency it is possible to create a T-jump induced difference spectrum from 50ns to 0.5ms. This study demonstrates the power of the dual time-resolved T-jump fluorescence and IR spectroscopy to resolve complex folding mechanisms by complementary IR absorbance and fluorescence measurements of protein dynamics.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
| | - Michael J Reddish
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States.
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30
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Lin CW, Gai F. Microscopic nucleation and propagation rates of an alanine-based α-helix. Phys Chem Chem Phys 2017; 19:5028-5036. [PMID: 28165082 PMCID: PMC5359971 DOI: 10.1039/c6cp08924k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An infrared temperature-jump (T-jump) study by Huang et al. (Proc. Natl. Acad. Sci. U. S. A., 2002, 99, 2788-2793) showed that the conformational relaxation kinetics of an alanine-based α-helical peptide depend not only on the final temperature (Tf) but also on the initial temperature (Ti) when Tf is fixed. Their finding indicates that the folding free energy landscape of this peptide is non-two-state like, allowing for the population of conformational ensembles with different helical lengths and relaxation times in the temperature range of the experiment. Because α-helix folding involves two fundamental events, nucleation and propagation, the results of Huang et al. thus present a unique opportunity to determine their rate constants - a long-sought goal in the study of the helix-coil transition dynamics. Herein, we capitalize on this notion and develop a coarse-grained kinetic model to globally fit the thermal unfolding curve and T-jump kinetic traces of this peptide. Using this strategy, we are able to explicitly determine the microscopic rate constants of the kinetic steps encountered in the nucleation and propagation processes. Our results reveal that the time taken to form one α-helical turn (i.e., an α-helical segment with one helical hydrogen bond) is about 315 ns, whereas the time taken to elongate this nucleus by one residue (or backbone unit) is 5.9 ns, depending on the position of the residue.
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Affiliation(s)
- Chun-Wei Lin
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, USA.
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31
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Yeh YQ, Liao KF, Shih O, Shiu YJ, Wu WR, Su CJ, Lin PC, Jeng US. Probing the Acid-Induced Packing Structure Changes of the Molten Globule Domains of a Protein near Equilibrium Unfolding. J Phys Chem Lett 2017; 8:470-477. [PMID: 28067527 DOI: 10.1021/acs.jpclett.6b02722] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Using simultaneously scanning small-angle X-ray scattering (SAXS) and UV-vis absorption with integrated online size exclusion chromatography, supplemental with molecular dynamics simulations, we unveil the long-postulated global structure evolution of a model multidomain protein bovine serum albumin (BSA) during acid-induced unfolding. Our results differentiate three global packing structures of the three molten globule domains of BSA, forming three intermediates I1, I2, and E along the unfolding pathway. The I1-I2 transition, overlooked in all previous studies, involves mainly coordinated reorientations across interconnected molten globule subdomains, and the transition activates a critical pivot domain opening of the protein for entering into the E form, with an unexpectedly large unfolding free energy change of -9.5 kcal mol-1, extracted based on the observed packing structural changes. The revealed local packing flexibility and rigidity of the molten globule domains in the E form elucidate how collective motions of the molten globule domains profoundly influence the folding-unfolding pathway of a multidomain protein.
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Affiliation(s)
- Yi-Qi Yeh
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Kuei-Fen Liao
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Ying-Jen Shiu
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Wei-Ru Wu
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Po-Chang Lin
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
- Department of Chemical Engineering, National Tsing Hua University , Hsinchu 30013, Taiwan
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32
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Ahmed IA, Gai F. Simple method to introduce an ester infrared probe into proteins. Protein Sci 2017; 26:375-381. [PMID: 27813296 DOI: 10.1002/pro.3076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 01/09/2023]
Abstract
The ester carbonyl stretching vibration has recently been shown to be a sensitive and convenient infrared (IR) probe of protein electrostatics due to the linear dependence of its frequency on local electric field. While an ester moiety can be easily incorporated into peptides via solid-phase synthesis, currently there is no method available to site-specifically incorporate it into a large protein. Herein, we show that it is possible to use a cysteine alkylation reaction to achieve this goal and demonstrate the feasibility of this simple method by successfully incorporating a methyl ester group (CH2 COOCH3 ) into a model peptide (YGGCGG), two amyloid-forming peptides derived from the insulin B chain and Aβ, and bovine serum albumin (BSA). IR results obtained with those peptide and protein systems further confirm the utility of this vibrational probe in monitoring, for example, the structural integrity of amyloid fibrils and ligand binding-induced changes in protein local hydration status.
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Affiliation(s)
- Ismail A Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
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33
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Oh KI, Smith-Dupont KB, Markiewicz BN, Gai F. Kinetics of peptide folding in lipid membranes. Biopolymers 2016; 104:281-90. [PMID: 25808575 DOI: 10.1002/bip.22640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/12/2015] [Accepted: 02/14/2015] [Indexed: 12/31/2022]
Abstract
Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Kathryn B Smith-Dupont
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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34
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Ding B, Hilaire MR, Gai F. Infrared and Fluorescence Assessment of Protein Dynamics: From Folding to Function. J Phys Chem B 2016; 120:5103-13. [PMID: 27183318 DOI: 10.1021/acs.jpcb.6b03199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
While folding or performing functions, a protein can sample a rich set of conformational space. However, experimentally capturing all of the important motions with sufficient detail to allow a mechanistic description of their dynamics is nontrivial since such conformational events often occur over a wide range of time and length scales. Therefore, many methods have been employed to assess protein conformational dynamics, and depending on the nature of the conformational transition in question, some may be more advantageous than others. Herein, we describe our recent efforts, and also those of others, wherever appropriate, to use infrared- and fluorescence-based techniques to interrogate protein folding and functional dynamics. Specifically, we focus on discussing how to use extrinsic spectroscopic probes to enhance the structural resolution of these techniques and how to exploit various cross-linking strategies to acquire dynamic and mechanistic information that was previously difficult to attain.
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Affiliation(s)
- Bei Ding
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Mary Rose Hilaire
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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35
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Abaskharon RM, Gai F. Direct measurement of the tryptophan-mediated photocleavage kinetics of a protein disulfide bond. Phys Chem Chem Phys 2016; 18:9602-7. [PMID: 26997094 PMCID: PMC4814302 DOI: 10.1039/c6cp00865h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Disulfide cleavage is one of the major causes underlying ultraviolet (UV) light-induced protein damage. While previous studies have provided strong evidence to support the notion that this process is mediated by photo-induced electron transfer from the excited state of an aromatic residue (e.g., tryptophan) to the disulfide bond, many mechanistic details are still lacking. For example, we do not know how quickly this process occurs in a protein environment. Herein, we design an experiment, which uses the unfolding kinetics of a protein as an observable, to directly assess the kinetics and mechanism of photo-induced disulfide cleavage. Our results show that this disulfide bond cleavage event takes place in ∼2 μs via a mechanism involving electron transfer from the triplet state of a tryptophan (Trp) residue to the disulfide bond. Furthermore, we find that one of the photoproducts of this reaction, a Trp-SR adduct, is formed locally, thus preventing the protein from re-cross-linking. Taken together, these findings suggest that a Trp-disulfide pair could be used as a photo-trigger to initiate protein folding dynamics and control the biological activities of disulfide-containing peptides.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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36
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Kim H, Kim S, Jung Y, Han J, Yun JH, Chang I, Lee W. Probing the Folding-Unfolding Transition of a Thermophilic Protein, MTH1880. PLoS One 2016; 11:e0145853. [PMID: 26766214 PMCID: PMC4713090 DOI: 10.1371/journal.pone.0145853] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
The folding mechanism of typical proteins has been studied widely, while our understanding of the origin of the high stability of thermophilic proteins is still elusive. Of particular interest is how an atypical thermophilic protein with a novel fold maintains its structure and stability under extreme conditions. Folding-unfolding transitions of MTH1880, a thermophilic protein from Methanobacterium thermoautotrophicum, induced by heat, urea, and GdnHCl, were investigated using spectroscopic techniques including circular dichorism, fluorescence, NMR combined with molecular dynamics (MD) simulations. Our results suggest that MTH1880 undergoes a two-state N to D transition and it is extremely stable against temperature and denaturants. The reversibility of refolding was confirmed by spectroscopic methods and size exclusion chromatography. We found that the hyper-stability of the thermophilic MTH1880 protein originates from an extensive network of both electrostatic and hydrophobic interactions coordinated by the central β-sheet. Spectroscopic measurements, in combination with computational simulations, have helped to clarify the thermodynamic and structural basis for hyper-stability of the novel thermophilic protein MTH1880.
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Affiliation(s)
- Heeyoun Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Sangyeol Kim
- Department of Physics, Pusan National University, Busan, 609–735, Korea
- Center for Proteome Biophysics, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 711–873, Korea
| | - Youngjin Jung
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Jeongmin Han
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Ji-Hye Yun
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Iksoo Chang
- Center for Proteome Biophysics, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 711–873, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, 711–873, Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
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37
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Seaiby C, Zabuga AV, Svendsen A, Rizzo TR. IR-induced conformational isomerization of a helical peptide in a cold ion trap. J Chem Phys 2016; 144:014304. [DOI: 10.1063/1.4939528] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Caroline Seaiby
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Aleksandra V. Zabuga
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Annette Svendsen
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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38
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Baiz CR, Tokmakoff A. Structural disorder of folded proteins: isotope-edited 2D IR spectroscopy and Markov state modeling. Biophys J 2016; 108:1747-1757. [PMID: 25863066 DOI: 10.1016/j.bpj.2014.12.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/05/2014] [Accepted: 12/19/2014] [Indexed: 01/14/2023] Open
Abstract
The conformational heterogeneity of the N-terminal domain of the ribosomal protein L9 (NTL91-39) in its folded state is investigated using isotope-edited two-dimensional infrared spectroscopy. Backbone carbonyls are isotope-labeled ((13)C=(18)O) at five selected positions (V3, V9, V9G13, G16, and G24) to provide a set of localized spectroscopic probes of the structure and solvent exposure at these positions. Structural interpretation of the amide I line shapes is enabled by spectral simulations carried out on structures extracted from a recent Markov state model. The V3 label spectrum indicates that the β-sheet contacts between strands I and II are well folded with minimal disorder. The V9 and V9G13 label spectra, which directly probe the hydrogen-bond contacts across the β-turn, show significant disorder, indicating that molecular dynamics simulations tend to overstabilize ideally folded β-turn structures in NTL91-39. In addition, G24-label spectra provide evidence for a partially disordered α-helix backbone that participates in hydrogen bonding with the surrounding water.
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Affiliation(s)
- Carlos R Baiz
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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39
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Oh KI, Fiorin G, Gai F. How Sensitive is the Amide I Vibration of the Polypeptide Backbone to Electric Fields? Chemphyschem 2015; 16:3595-8. [PMID: 26419214 DOI: 10.1002/cphc.201500777] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Indexed: 01/05/2023]
Abstract
Site-selective isotopic labeling of amide carbonyls offers a nonperturbative means to introduce a localized infrared probe into proteins. Although this strategy has been widely used to investigate various biological questions, the dependence of the underlying amide I vibrational frequency on electric fields (or Stark tuning rate) has not been fully determined, which prevents it from being used in a quantitative manner in certain applications. Herein, through the use of experiments and molecular dynamics simulations, the Stark tuning rate of the amide I vibration of an isotopically labeled backbone carbonyl in a transmembrane α-helix is determined to be approximately 1.4 cm(-1) /(MV/cm). This result provides a quantitative basis for using this vibrational model to assess local electric fields in proteins, among other applications. For instance, by using this value, we are able to show that the backbone region of a dipeptide has a surprisingly low dielectric constant.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA, 19104-6323, USA
| | - Giacomo Fiorin
- Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, PA, 19122-1801, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA, 19104-6323, USA.
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40
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Fang B, Wang T, Chen X, Jin T, Zhang R, Zhuang W. Modeling Vibrational Spectra of Ester Carbonyl Stretch in Water and DMSO Based on Molecular Dynamics Simulation. J Phys Chem B 2015; 119:12390-6. [PMID: 26335032 DOI: 10.1021/acs.jpcb.5b06541] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of molecular dynamics simulation, we model the ester carbonyl stretch FTIR signals of methyl acetate in D2O and DMSO. An ab initio map is constructed at the B3LYP/6-311++G** level to relate the carbonyl stretch frequency to the external electric field. Using this map, fluctuating Hamiltonian of the carbonyl stretch is constructed from the MD simulation trajectory. The IR spectra calculated based on this Hamiltonian are found to be in good agreement with the experiment. For methyl acetate in D2O, hydrogen bonding on alkoxy oxygen causes a blue shift of frequency, while that on carbonyl oxygen causes a red shift. Two peaks observed in FTIR signals originate from the balance of these two effects. Furthermore, in both D2O and DMSO solutions, correlations are found between the instantaneous electric field on C═O and the frequencies. Broader line width of the signal in D2O suggests a more inhomogeneous electric field distribution due to the complicated hydrogen-bonding environment.
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Affiliation(s)
- Bin Fang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Tianjun Wang
- Department of Chemistry, ShanghaiTech University , 19 Yueyang Road, Shanghai 200031, China
| | - Xian Chen
- Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), Department of Physics, Jilin University , 2699 Qianjin Street, ChangChun 130012, China
| | - Tan Jin
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Ruiting Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
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41
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Hilaire MR, Abaskharon RM, Gai F. Biomolecular Crowding Arising from Small Molecules, Molecular Constraints, Surface Packing, and Nano-Confinement. J Phys Chem Lett 2015; 6:2546-53. [PMID: 26266732 PMCID: PMC4610718 DOI: 10.1021/acs.jpclett.5b00957] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The effect of macromolecular crowding on the structure, dynamics, and reactivity of biomolecules is well established and the relevant research has been extensively reviewed. Herein, we focus our discussion on crowding effects arising from small cosolvent molecules and densely packed surface conditions. In addition, we highlight recent efforts that capitalize on the excluded volume effect for various tailored biochemical and biophysical applications. Specifically, we discuss how a targeted increase in local mass density can be exploited to gain insight into the folding dynamics of the protein of interest and how confinement via reverse micelles can be used to study a range of biophysical questions, from protein hydration dynamics to amyloid formation.
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Affiliation(s)
| | | | - Feng Gai
- To whom correspondence should be addressed; ; Phone: 215-573-6256; Fax: 215-573-2112
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42
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Sborgi L, Verma A, Piana S, Lindorff-Larsen K, Cerminara M, Santiveri C, Shaw DE, de Alba E, Muñoz V. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations. J Am Chem Soc 2015; 137:6506-16. [PMID: 25924808 PMCID: PMC4648500 DOI: 10.1021/jacs.5b02324] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 03/04/2015] [Indexed: 01/02/2023]
Abstract
The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulations to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooperative equilibrium unfolding behavior. Experiments and simulations expose a remarkably complex pattern of structural changes that occur at the atomic level and from which the detailed network of residue-residue couplings associated with cooperative folding emerges. Such thermodynamic residue-residue couplings appear to be linked to the order of mechanistically significant events that take place during the folding process. Our results on gpW indicate that the methods employed in this study are likely to prove broadly applicable to the fine analysis of folding mechanisms in fast folding proteins.
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Affiliation(s)
- Lorenzo Sborgi
- National
Biotechnology Center, CSIC, Madrid 28049, Spain
| | - Abhinav Verma
- National
Biotechnology Center, CSIC, Madrid 28049, Spain
| | - Stefano Piana
- D.
E. Shaw Research, New York, New York 10036, United States
| | | | | | | | - David E. Shaw
- D.
E. Shaw Research, New York, New York 10036, United States
- Department
of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| | - Eva de Alba
- National
Biotechnology Center, CSIC, Madrid 28049, Spain
| | - Victor Muñoz
- National
Biotechnology Center, CSIC, Madrid 28049, Spain
- School
of Engineering, University of California, Merced, California 95343, United States
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43
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Pazos IM, Ahmed IA, Berríos MIL, Gai F. Sensing pH via p-cyanophenylalanine fluorescence: Application to determine peptide pKa and membrane penetration kinetics. Anal Biochem 2015; 483:21-6. [PMID: 25935260 DOI: 10.1016/j.ab.2015.04.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 12/22/2022]
Abstract
We expand the spectroscopic utility of a well-known infrared and fluorescence probe, p-cyanophenylalanine, by showing that it can also serve as a pH sensor. This new application is based on the notion that the fluorescence quantum yield of this unnatural amino acid, when placed at or near the N-terminal end of a polypeptide, depends on the protonation status of the N-terminal amino group of the peptide. Using this pH sensor, we are able to determine the N-terminal pKa values of nine tripeptides and also the membrane penetration kinetics of a cell-penetrating peptide. Taken together, these examples demonstrate the applicability of using this unnatural amino acid fluorophore to study pH-dependent biological processes or events that accompany a pH change.
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Affiliation(s)
- Ileana M Pazos
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ismail A Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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44
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Guidez EB, Gordon MS. Dispersion Correction Derived from First Principles for Density Functional Theory and Hartree–Fock Theory. J Phys Chem A 2015; 119:2161-8. [DOI: 10.1021/acs.jpca.5b00379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emilie B. Guidez
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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45
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Markiewicz BN, Culik RM, Gai F. Tightening up the structure, lighting up the pathway: Application of molecular constraints and light to manipulate protein folding, self-assembly and function. Sci China Chem 2014; 57:1615-1624. [PMID: 25722715 PMCID: PMC4337807 DOI: 10.1007/s11426-014-5225-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chemical cross-linking provides an effective avenue to reduce the conformational entropy of polypeptide chains and hence has become a popular method to induce or force structural formation in peptides and proteins. Recently, other types of molecular constraints, especially photoresponsive linkers and functional groups, have also found increased use in a wide variety of applications. Herein, we provide a concise review of using various forms of molecular strategies to constrain proteins, thereby stabilizing their native states, gaining insight into their folding mechanisms, and/or providing a handle to trigger a conformational process of interest with light. The applications discussed here cover a wide range of topics, ranging from delineating the details of the protein folding energy landscape to controlling protein assembly and function.
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Affiliation(s)
| | - Robert M. Culik
- Department of Biochemistry and Biophysics, University of Pennsylvania, PA, 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, PA, 19104, USA
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46
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Baiz CR, Lin YS, Peng CS, Beauchamp KA, Voelz VA, Pande VS, Tokmakoff A. A molecular interpretation of 2D IR protein folding experiments with Markov state models. Biophys J 2014; 106:1359-70. [PMID: 24655511 DOI: 10.1016/j.bpj.2014.02.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 01/28/2014] [Accepted: 02/03/2014] [Indexed: 11/24/2022] Open
Abstract
The folding mechanism of the N-terminal domain of ribosomal protein L9 (NTL91-39) is studied using temperature-jump (T-jump) amide I' two-dimensional infrared (2D IR) spectroscopy in combination with spectral simulations based on a Markov state model (MSM) built from millisecond-long molecular dynamics trajectories. The results provide evidence for a compact well-structured folded state and a heterogeneous fast-exchanging denatured state ensemble exhibiting residual secondary structure. The folding rate of 26.4 μs(-1) (at 80°C), extracted from the T-jump response of NTL91-39, compares favorably with the 18 μs(-1) obtained from the MSM. Structural decomposition of the MSM and analysis along the folding coordinate indicates that helix-formation nucleates the global folding. Simulated difference spectra, corresponding to the global folding transition of the MSM, are in qualitative agreement with measured T-jump 2D IR spectra. The experiments demonstrate the use of T-jump 2D IR spectroscopy as a valuable tool for studying protein folding, with direct connections to simulations. The results suggest that in addition to predicting the correct native structure and folding time constant, molecular dynamics simulations carried out with modern force fields provide an accurate description of folding mechanisms in small proteins.
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Affiliation(s)
- Carlos R Baiz
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Yu-Shan Lin
- Department of Chemistry, Stanford University, Stanford, California
| | - Chunte Sam Peng
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania
| | - Vijay S Pande
- Department of Chemistry, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California; Department of Structural Biology, Stanford University, Stanford, California
| | - Andrei Tokmakoff
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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47
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Novel microscale approaches for easy, rapid determination of protein stability in academic and commercial settings. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2241-50. [PMID: 25262836 PMCID: PMC4332417 DOI: 10.1016/j.bbapap.2014.09.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/04/2014] [Accepted: 09/18/2014] [Indexed: 01/26/2023]
Abstract
Chemical denaturant titrations can be used to accurately determine protein stability. However, data acquisition is typically labour intensive, has low throughput and is difficult to automate. These factors, combined with high protein consumption, have limited the adoption of chemical denaturant titrations in commercial settings. Thermal denaturation assays can be automated, sometimes with very high throughput. However, thermal denaturation assays are incompatible with proteins that aggregate at high temperatures and large extrapolation of stability parameters to physiological temperatures can introduce significant uncertainties. We used capillary-based instruments to measure chemical denaturant titrations by intrinsic fluorescence and microscale thermophoresis. This allowed higher throughput, consumed several hundred-fold less protein than conventional, cuvette-based methods yet maintained the high quality of the conventional approaches. We also established efficient strategies for automated, direct determination of protein stability at a range of temperatures via chemical denaturation, which has utility for characterising stability for proteins that are difficult to purify in high yield. This approach may also have merit for proteins that irreversibly denature or aggregate in classical thermal denaturation assays. We also developed procedures for affinity ranking of protein–ligand interactions from ligand-induced changes in chemical denaturation data, and proved the principle for this by correctly ranking the affinity of previously unreported peptide–PDZ domain interactions. The increased throughput, automation and low protein consumption of protein stability determinations afforded by using capillary-based methods to measure denaturant titrations, can help to revolutionise protein research. We believe that the strategies reported are likely to find wide applications in academia, biotherapeutic formulation and drug discovery programmes. Chemical denaturant titrations are slow, lengthy and consume lots of protein sample. We developed very fast methods for measuring chemical denaturant titrations. Automated titrations can be measured in minutes using only μl sample volumes. Ligand interactions rapidly screened and ranked via changes in protein stability These advances make chemical denaturation more suitable for commercial research.
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48
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Culik RM, Abaskharon RM, Pazos IM, Gai F. Experimental validation of the role of trifluoroethanol as a nanocrowder. J Phys Chem B 2014; 118:11455-61. [PMID: 25215518 PMCID: PMC4183368 DOI: 10.1021/jp508056w] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Trifluoroethanol
(TFE) is commonly used to induce protein secondary
structure, especially α-helix formation. Due to its amphiphilic
nature, however, TFE can also self-associate to form micellelike,
nanometer-sized clusters. Herein, we hypothesize that such clusters
can act as nanocrowders to increase protein folding rates via the
excluded volume effect. To test this hypothesis, we measure the conformational
relaxation kinetics of an intrinsically disordered protein, the phosphorylated
kinase inducible domain (pKID), which forms a helix–turn–helix
in TFE solutions. We find that the conformational relaxation rate
of pKID displays a rather complex dependence on TFE percentage (v/v):
while it first decreases between 0 and 5%, between 5 and 15% the rate
increases and then remains relatively unchanged between 15 and 30%
and finally decreases again at higher percentages (i.e., 50%). This
trend coincides with the fact that TFE clustering is maximized in
the range of 15–30%, thus providing validation of our hypothesis.
Another line of supporting evidence comes from the observation that
the relaxation rate of a monomeric helical peptide, which due to its
predominantly local interactions in the folded state is less affected
by crowding, does not show a similar TFE dependence.
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Affiliation(s)
- Robert M Culik
- Department of Biochemistry & Biophysics and ‡Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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49
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Jones EM, Balakrishnan G, Squier TC, Spiro TG. Distinguishing unfolding and functional conformational transitions of calmodulin using ultraviolet resonance Raman spectroscopy. Protein Sci 2014; 23:1094-101. [PMID: 24895328 DOI: 10.1002/pro.2495] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 01/09/2023]
Abstract
Calmodulin (CaM) is a ubiquitous moderator protein for calcium signaling in all eukaryotic cells. This small calcium-binding protein exhibits a broad range of structural transitions, including domain opening and folding-unfolding, that allow it to recognize a wide variety of binding partners in vivo. While the static structures of CaM associated with its various binding activities are fairly well-known, it has been challenging to examine the dynamics of transition between these structures in real-time, due to a lack of suitable spectroscopic probes of CaM structure. In this article, we examine the potential of ultraviolet resonance Raman (UVRR) spectroscopy for clarifying the nature of structural transitions in CaM. We find that the UVRR spectral change (with 229 nm excitation) due to thermal unfolding of CaM is qualitatively different from that associated with opening of the C-terminal domain in response to Ca(2+) binding. This spectral difference is entirely due to differences in tertiary contacts at the interdomain tyrosine residue Tyr138, toward which other spectroscopic methods are not sensitive. We conclude that UVRR is ideally suited to identifying the different types of structural transitions in CaM and other proteins with conformation-sensitive tyrosine residues, opening a path to time-resolved studies of CaM dynamics using Raman spectroscopy.
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Affiliation(s)
- Eric M Jones
- Department of Chemistry, University of Washington, Seattle, Washington, 98195-1700
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Pazos IM, Ghosh A, Tucker MJ, Gai F. Ester carbonyl vibration as a sensitive probe of protein local electric field. Angew Chem Int Ed Engl 2014; 53:6080-4. [PMID: 24788907 PMCID: PMC4104746 DOI: 10.1002/anie.201402011] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 03/20/2014] [Indexed: 11/10/2022]
Abstract
The ability to quantify the local electrostatic environment of proteins and protein/peptide assemblies is key to gaining a microscopic understanding of many biological interactions and processes. Herein, we show that the ester carbonyl stretching vibration of two non-natural amino acids, L-aspartic acid 4-methyl ester and L-glutamic acid 5-methyl ester, is a convenient and sensitive probe in this regard, since its frequency correlates linearly with the local electrostatic field for both hydrogen-bonding and non-hydrogen-bonding environments. We expect that the resultant frequency-electric-field map will find use in various applications. Furthermore, we show that, when situated in a non-hydrogen-bonding environment, this probe can also be used to measure the local dielectric constant (ε). For example, its application to amyloid fibrils formed by Aβ(16-22) revealed that the interior of such β-sheet assemblies has an ε value of approximately 5.6.
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Affiliation(s)
- Ileana M. Pazos
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street, Philadelphia, PA 19104, United States
| | - Ayanjeet Ghosh
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street, Philadelphia, PA 19104, United States
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street, Philadelphia, PA 19104, United States
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