1
|
Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024. [PMID: 38959423 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
Collapse
Affiliation(s)
- Zachary Birch-Price
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Florence J Hardy
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Thomas M Lister
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Anna R Kohn
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| |
Collapse
|
2
|
Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [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: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
Collapse
Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
3
|
Lin Y, Horne WS. Backbone Modification in a Protein Hydrophobic Core. Chemistry 2024:e202401890. [PMID: 38753977 DOI: 10.1002/chem.202401890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 05/18/2024]
Abstract
Targeted protein backbone modification can recreate tertiary structures reminiscent of folds found in nature on artificial scaffolds with improved biostability. Incorporation of altered monomers in such entities is typically limited to sites distant from the hydrophobic core to avoid potential disruptions to folding. This is limiting, as it is advantageous in some applications to incorporate artificial connectivity at buried sites. Here, we report an examination of protein backbone modification targeted specifically to hydrophobic core positions and its impacts on tertiary folded structure and fold stability. Different artificial monomer types are placed at core, core-flanking, or solvent-exposed positions in a compact three-helix protein. Effects on structure and folding energetics are assessed by NMR spectroscopy and biophysical methods. Results show that artificial residues can be well accommodated in the hydrophobic core of a defined tertiary fold, with effects on stability only modestly larger than identical changes at solvent-exposed sites. Collectively, these results provide new insights into folding behavior of protein-like artificial chains as well as strategies for the design of such molecules.
Collapse
Affiliation(s)
- Yuhan Lin
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA
| |
Collapse
|
4
|
Zhou L, Feng RR, Zhang W, Gai F. Triple-Bond Vibrations: Emerging Applications in Energy and Biological Sciences. J Phys Chem Lett 2024; 15:187-200. [PMID: 38156972 DOI: 10.1021/acs.jpclett.3c02619] [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: 01/03/2024]
Abstract
Triple bonds, such as that formed between two carbon atoms (i.e., C≡C) or that formed between one carbon atom and one nitrogen atom (i.e., C≡N), afford unique chemical bonding and hence vibrational characteristics. As such, they are not only frequently used to construct molecules with tailored chemical and/or physical properties but also employed as vibrational probes to provide site-specific chemical and/or physical information at the molecular level. Herein, we offer our perspective on the emerging applications of various triple-bond vibrations in energy and biological sciences with a focus on C≡C and C≡N triple bonds.
Collapse
Affiliation(s)
- Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
5
|
Hunt NT. Biomolecular infrared spectroscopy: making time for dynamics. Chem Sci 2024; 15:414-430. [PMID: 38179520 PMCID: PMC10763549 DOI: 10.1039/d3sc05223k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.
Collapse
Affiliation(s)
- Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York Heslington York YO10 5DD UK
| |
Collapse
|
6
|
Brüggemann J, Chekmeneva M, Wolter M, Jacob CR. Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra. J Phys Chem Lett 2023; 14:9257-9264. [PMID: 37812580 PMCID: PMC10591501 DOI: 10.1021/acs.jpclett.3c02662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and β-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.
Collapse
Affiliation(s)
- Julia Brüggemann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Maria Chekmeneva
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| |
Collapse
|
7
|
Brüggemann J, Wolter M, Jacob CR. Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI. J Chem Phys 2022; 157:244107. [PMID: 36586972 DOI: 10.1063/5.0135273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models which require an empirical parameterization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF)/vibrational configuration interaction (L-VCI) approach previously established for (linear) anharmonic theoretical vibrational spectroscopy [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365-3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parameterization of vibrational exciton models for predicting 2D IR spectra.
Collapse
Affiliation(s)
- Julia Brüggemann
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| |
Collapse
|
8
|
Liu J, Feng RR, Zhou L, Gai F, Zhang W. Photoenhancement of the C≡N Stretching Vibration Intensity of Aromatic Nitriles. J Phys Chem Lett 2022; 13:9745-9751. [PMID: 36222647 DOI: 10.1021/acs.jpclett.2c02418] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The C≡N stretching vibration is a versatile infrared (IR) reporter that is useful for a wide range of applications. Aiming to further expand its spectroscopic utility, herein, we show that, using 4-cyanoindole and 4-cyano-7-azaindole as examples, photoexcitation can significantly shift the frequency (νCN) and enhance the molar extinction coefficient (εCN) of this vibrational mode of aromatic nitriles and that, for these indole derivatives, the enhancement factor can reach 13. Moreover, we find that while solvent relaxation at the excited electronic state(s) always leads to an increase in εCN, its effect on νCN depends on the solute and the solvent. Taken together, these results demonstrate that solvent relaxation can differently affect the local environment of the nitrile group and its conjugation with the indole ring and, more importantly, that the C≡N stretching vibration can serve as a sensitive IR probe of charge and electron transfer processes in which an aromatic nitrile is involved.
Collapse
Affiliation(s)
- Jingsong Liu
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
9
|
Thielges MC. Transparent window 2D IR spectroscopy of proteins. J Chem Phys 2021; 155:040903. [PMID: 34340394 PMCID: PMC8302233 DOI: 10.1063/5.0052628] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
Proteins are complex, heterogeneous macromolecules that exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires experimental tools to characterize them with high spatial and temporal precision. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution. Two-dimensional (2D) IR methods that provide richer information are becoming more routine but remain challenging to apply to proteins. Spectral congestion typically prevents selective investigation of native vibrations; however, the problem can be overcome by site-specific introduction of amino acid side chains that have vibrational groups with frequencies in the "transparent window" of protein spectra. This Perspective provides an overview of the history and recent progress in the development of transparent window 2D IR of proteins.
Collapse
Affiliation(s)
- Megan C. Thielges
- Department of Chemistry, Indiana University, Bloomington,
Indiana 47405, USA
| |
Collapse
|
10
|
Tumbic GW, Hossan MY, Thielges MC. Protein Dynamics by Two-Dimensional Infrared Spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:299-321. [PMID: 34314221 PMCID: PMC8713465 DOI: 10.1146/annurev-anchem-091520-091009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.
Collapse
Affiliation(s)
- Goran W Tumbic
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Md Yeathad Hossan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| |
Collapse
|
11
|
Watson MD, Lee JC. Coupling chemical biology and vibrational spectroscopy for studies of amyloids in vitro and in cells. Curr Opin Chem Biol 2021; 64:90-97. [PMID: 34186291 DOI: 10.1016/j.cbpa.2021.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/04/2021] [Accepted: 05/18/2021] [Indexed: 01/21/2023]
Abstract
Amyloid diseases are characterized by the aggregation of various proteins to form insoluble β-sheet-rich fibrils leading to cell death. Vibrational spectroscopies have emerged as attractive methods to study this process because of the rich structural information that can be extracted without large, perturbative probes. Importantly, specific vibrations such as the amide-I band directly report on secondary structure changes, which are key features of amyloid formation. Beyond intrinsic vibrations, the incorporation of unnatural vibrational probes can improve sensitivity for secondary structure determination (e.g. isotopic labeling), can provide residue-specific information of the surrounding polarity (e.g. unnatural amino acid), and are translatable into cellular studies. Here, we review the latest studies that have leveraged tools from chemical biology for the incorporation of novel vibrational probes into amyloidogenic proteins for both mechanistic and cellular studies.
Collapse
Affiliation(s)
- Matthew D Watson
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
12
|
Yoon A, Zhen J, Guo Z. Segmental structural dynamics in Aβ42 globulomers. Biochem Biophys Res Commun 2021; 545:119-124. [PMID: 33548624 DOI: 10.1016/j.bbrc.2021.01.081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/23/2021] [Indexed: 02/06/2023]
Abstract
Aβ42 aggregation plays a central role in the pathogenesis of Alzheimer's disease. In addition to the insoluble fibrils that comprise the amyloid plaques, Aβ42 also forms soluble aggregates collectively called oligomers, which are more toxic and pathogenic than fibrils. Understanding the structure and dynamics of Aβ42 oligomers is critical for developing effective therapeutic interventions against these oligomers. Here we studied the structural dynamics of Aβ42 globulomers, a type of Aβ42 oligomers prepared in the presence of sodium dodecyl sulfate, using site-directed spin labeling. Spin labels were introduced, one at a time, at all 42 residue positions of Aβ42 sequence. Electron paramagnetic resonance spectra of spin-labeled samples reveal four structural segments based on site-dependent spin label mobility pattern. Segment-1 consists of residues 1-6, which have the highest mobility that is consistent with complete disorder. Segment-3 is the most immobilized region, including residues 31-34. Segment-2 and -4 have intermediate mobility and are composed of residues 7-30 and 35-42, respectively. Considering the inverse relationship between protein dynamics and stability, our results suggest that residues 31-34 are the most stable segment in Aβ42 oligomers. At the same time, the EPR spectral lineshape suggests that Aβ42 globulomers lack a well-packed structural core akin to that of globular proteins.
Collapse
Affiliation(s)
- Allison Yoon
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - James Zhen
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
| |
Collapse
|
13
|
Abstract
This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.
Collapse
|
14
|
Schmidt-Engler JM, Zangl R, Guldan P, Morgner N, Bredenbeck J. Exploring the 2D-IR repertoire of the -SCN label to study site-resolved dynamics and solvation in the calcium sensor protein calmodulin. Phys Chem Chem Phys 2020; 22:5463-5475. [PMID: 32096510 DOI: 10.1039/c9cp06808b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The calcium sensor protein calmodulin is ubiquitous among eukaryotes. It translates intracellular Ca2+ influx (by a decrease of conformational flexibility) into increased target recognition affinity. Here we demonstrate that by using the IR reporter -SCN in combination with 2D-IR spectroscopy, global structure changes and local dynamics, degree of solvent exposure and protein-ligand interaction can be characterised in great detail. The long vibrational lifetime of the -SCN label allows for centerline slope analysis of the 2D-IR line shape up to 120 ps to deduce the frequency-frequency correlation function (FFCF) of the -SCN label in various states and label positions in the protein. Based on that we show clear differences between a solvent exposed site, the environment close to the Ca2+ binding motif and three highly conserved positions for ligand binding. Furthermore, we demonstrate how these dynamics are affected by conformational change induced by the addition of Ca2+ ions and by interaction with a short helical peptide mimicking protein binding. We show that the binding mode is strongly heterogeneous among the probed key binding methionine residues. SCN's vibrational relaxation is dominated by intermolecular contributions. Changes in the vibrational lifetime upon changing between H2O and D2O buffer therefore provide a robust measure for water accessibility of the label. Characterising -SCN's extinction coefficient, vibrational lifetime in light and heavy water and its FFCF we demonstrate the vast potential it has as a label especially for nonlinear spectroscopies, such as 2D-IR spectroscopy.
Collapse
Affiliation(s)
- Julian M Schmidt-Engler
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
| | - Rene Zangl
- Johann Wolfgang Goethe-University, Institute of Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Patrick Guldan
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
| | - Nina Morgner
- Johann Wolfgang Goethe-University, Institute of Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
| |
Collapse
|
15
|
Chalyavi F, Adeyiga O, Weiner JM, Monzy JN, Schmitz AJ, Nguyen JK, Fenlon EE, Brewer SH, Odoh SO, Tucker MJ. 2D-IR studies of cyanamides (NCN) as spectroscopic reporters of dynamics in biomolecules: Uncovering the origin of mysterious peaks. J Chem Phys 2020; 152:074201. [PMID: 32087671 PMCID: PMC7028433 DOI: 10.1063/1.5138654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/27/2020] [Indexed: 12/17/2022] Open
Abstract
Cyanamides (NCN) have been shown to have a larger transition dipole strength than cyano-probes. In addition, they have similar structural characteristics and vibrational lifetimes to the azido-group, suggesting their utility as infrared (IR) spectroscopic reporters for structural dynamics in biomolecules. To access the efficacy of NCN as an IR probe to capture the changes in the local environment, several model systems were evaluated via 2D IR spectroscopy. Previous work by Cho [G. Lee, D. Kossowska, J. Lim, S. Kim, H. Han, K. Kwak, and M. Cho, J. Phys. Chem. B 122(14), 4035-4044 (2018)] showed that phenylalanine analogues containing NCN show strong anharmonic coupling that can complicate the interpretation of structural dynamics. However, when NCN is embedded in 5-membered ring scaffolds, as in N-cyanomaleimide and N-cyanosuccinimide, a unique band structure is observed in the 2D IR spectrum that is not predicted by simple anharmonic frequency calculations. Further investigation indicated that electron delocalization plays a role in the origins of the band structure. In particular, the origin of the lower frequency transitions is likely a result of direct interaction with the solvent.
Collapse
Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Olajumoke Adeyiga
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Julia M. Weiner
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Judith N. Monzy
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Andrew J. Schmitz
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Justin K. Nguyen
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Edward E. Fenlon
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Samuel O. Odoh
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| |
Collapse
|
16
|
Schmidt-Engler JM, Blankenburg L, Zangl R, Hoffmann J, Morgner N, Bredenbeck J. Local dynamics of the photo-switchable protein PYP in ground and signalling state probed by 2D-IR spectroscopy of –SCN labels. Phys Chem Chem Phys 2020; 22:22963-22972. [DOI: 10.1039/d0cp04307a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ 2D-IR spectroscopy of the protein label –SCN to describe the local dynamics in the photo-switchable protein PYP in its dark state (pG) and after photoactivation, concomitant with vast structural rearrangements, in its signalling state (pB).
Collapse
Affiliation(s)
| | - Larissa Blankenburg
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Rene Zangl
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Jan Hoffmann
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Nina Morgner
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| |
Collapse
|
17
|
Vibrational Approach to the Dynamics and Structure of Protein Amyloids. Molecules 2019; 24:molecules24010186. [PMID: 30621325 PMCID: PMC6337179 DOI: 10.3390/molecules24010186] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features of the aggregates is critical for a comprehensive understanding of the mechanisms of protein oligomerization and fibrillization. Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation. We address the application of the vibrational approaches in recent studies of conformational dynamics and structural characteristics of protein oligomers and amyloid fibrils. In particular, introduction of isotope labelled carbonyl into a peptide backbone, and incorporation of the extrinsic unnatural amino acids with vibrational moieties on the side chain, have greatly expanded the ability of vibrational spectroscopy to obtain site-specific structural and dynamic information. The applications of these methods in recent studies of protein aggregation are also reviewed.
Collapse
|
18
|
Liu H, Morris C, Lantz R, Kent TW, Elbassal EA, Wojcikiewicz EP, Du D. Residue‐Specific Dynamics and Local Environmental Changes in Aβ40 Oligomer and Fibril Formation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Haiyang Liu
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Clifford Morris
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Richard Lantz
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Thomas W. Kent
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Esmail A. Elbassal
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Ewa P. Wojcikiewicz
- Department of Biomedical ScienceFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Deguo Du
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| |
Collapse
|
19
|
Liu H, Morris C, Lantz R, Kent TW, Elbassal EA, Wojcikiewicz EP, Du D. Residue-Specific Dynamics and Local Environmental Changes in Aβ40 Oligomer and Fibril Formation. Angew Chem Int Ed Engl 2018; 57:8017-8021. [PMID: 29750857 DOI: 10.1002/anie.201802490] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 11/12/2022]
Abstract
Elucidating local dynamics of protein aggregation is crucial for understanding the mechanistic details of protein amyloidogenesis. Herein, we studied the residue-specific dynamics and local environmental changes of Aβ40 along the course of aggregation by using para-cyanophenylalanine (PheCN ) as a fluorescent and vibrational probe. Our results show that the PheCN residues introduced at various positions all exhibited an immediate decay of fluorescence intensity, indicating a relatively synergistic process in early oligomer formation. The fast decreases in the fluorescence intensities of residues 19 and 20 in the central hydrophobic core region and residue 10 in the N-terminal region suggest that they play crucial roles in the formation of the oligomeric core. The PheCN 4 residue exhibits a remarkably slower decrease in fluorescence intensity, implicating its dynamic conformational characteristics in oligomer and fibril formation. Our results also suggest that the N-terminal residues in fibrils are surrounded by a relatively hydrophobic local environment, as opposed to being solvated.
Collapse
Affiliation(s)
- Haiyang Liu
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Clifford Morris
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Richard Lantz
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Thomas W Kent
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Esmail A Elbassal
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Ewa P Wojcikiewicz
- Department of Biomedical Science, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| |
Collapse
|
20
|
Lee G, Kossowska D, Lim J, Kim S, Han H, Kwak K, Cho M. Cyanamide as an Infrared Reporter: Comparison of Vibrational Properties between Nitriles Bonded to N and C Atoms. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.8b00887] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giseong Lee
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Joonhyung Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Soobin Kim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| |
Collapse
|
21
|
Ghosh A, Ostrander JS, Zanni MT. Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy. Chem Rev 2017; 117:10726-10759. [PMID: 28060489 PMCID: PMC5500453 DOI: 10.1021/acs.chemrev.6b00582] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins exhibit structural fluctuations over decades of time scales. From the picosecond side chain motions to aggregates that form over the course of minutes, characterizing protein structure over these vast lengths of time is important to understanding their function. In the past 15 years, two-dimensional infrared spectroscopy (2D IR) has been established as a versatile tool that can uniquely probe proteins structures on many time scales. In this review, we present some of the basic principles behind 2D IR and show how they have, and can, impact the field of protein biophysics. We highlight experiments in which 2D IR spectroscopy has provided structural and dynamical data that would be difficult to obtain with more standard structural biology techniques. We also highlight technological developments in 2D IR that continue to expand the scope of scientific problems that can be accessed in the biomedical sciences.
Collapse
Affiliation(s)
| | - Joshua S. Ostrander
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
22
|
Johnson PJM, Koziol KL, Hamm P. Quantifying Biomolecular Recognition with Site-Specific 2D Infrared Probes. J Phys Chem Lett 2017; 8:2280-2284. [PMID: 28471671 DOI: 10.1021/acs.jpclett.7b00742] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Azidohomoalanine (Aha) is an unnatural amino acid containing an infrared active azido side chain group that can, through frequency shifts of the azido stretch vibration, act as a probe of local structure. To realize the potential of such structural probes for protein science, we have developed a two-dimensional infrared spectrometer employing fast mechanical scanning and intrinsic phasing of the resulting spectra, leading to a lower sensitivity limit of ∼100 μOD level samples. Using this approach, we quantify the biomolecular recognition between a PDZ2 domain and two Aha-mutated peptides. It is shown that this method can distinguish different binding modes and that the energetics of binding can be determined.
Collapse
Affiliation(s)
- Philip J M Johnson
- Department of Chemistry, University of Zurich , Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Klemens L Koziol
- Department of Chemistry, University of Zurich , Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich , Winterthurerstr. 190, 8057 Zurich, Switzerland
| |
Collapse
|
23
|
Ramos S, Scott KJ, Horness RE, Le Sueur AL, Thielges MC. Extended timescale 2D IR probes of proteins: p-cyanoselenophenylalanine. Phys Chem Chem Phys 2017; 19:10081-10086. [PMID: 28367555 PMCID: PMC6252261 DOI: 10.1039/c7cp00403f] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The importance of dynamics to the function of proteins is well appreciated, but the difficulty in their measurement impedes investigation into their precise role(s). 2D IR spectroscopy is a developing approach for the study of dynamics and has motivated efforts to develop spectrally resolved IR probe groups that enable its application for measuring the dynamics at specific sites in a protein. A challenge with this approach is that the timescales accessible are limited by the vibrational lifetimes of the probes. Toward development of better probes for 2D IR spectroscopy of protein dynamics, we report the characterization of p-cyano-seleno-phenylalanine (CNSePhe), a derivative of the well established IR probe p-cyano-phenylalanine (CNPhe), by FT IR, pump-probe, and 2D IR spectroscopy. The incorporation of the heavy Se atom decouples the CN vibration from the rest in the molecule. Although this leads to a reduction of the transition dipole strength, and thus a reduction in signal intensity, it also dramatically increases the vibrational lifetime, enabling collection of 2D IR spectra for analysis of molecular dynamics on much longer timescales. Interestingly, we also find that the lifetime for CNSePhe shows increased sensitivity to the presence of hydrogen bonding interactions with the CN, suggesting that the probe should be useful for interpretation of CN spectra and possibly for the study of solvation.
Collapse
Affiliation(s)
- S. Ramos
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - K. J. Scott
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - R. E. Horness
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - A. L. Le Sueur
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - M. C. Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| |
Collapse
|
24
|
Abaskharon RM, Brown SP, Zhang W, Chen J, Smith AB, Gai F. Isotope-Labeled Aspartate Sidechain as a Non-Perturbing Infrared Probe: Application to Investigate the Dynamics of a Carboxylate Buried Inside a Protein. Chem Phys Lett 2017; 683:193-198. [PMID: 29033461 DOI: 10.1016/j.cplett.2017.03.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Because of their negatively charged carboxylates, aspartate and glutamate are frequently found at the active or binding site of proteins. However, studying a specific carboxylate in proteins that contain multiple aspartates and/or glutamates via infrared spectroscopy is difficult due to spectral overlap. We show, herein, that isotopic-labeling of the aspartate sidechain can overcome this limitation as the resultant 13C=O asymmetric stretching vibration resides in a transparent region of the protein IR spectrum. Applicability of this site-specific vibrational probe is demonstrated by using it to assess the dynamics of an aspartate ion buried inside a small protein via two-dimensional infrared spectroscopy.
Collapse
Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Stephen P Brown
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Wenkai Zhang
- Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Jianxin Chen
- Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA.,Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| |
Collapse
|
25
|
Johnson PJM, Koziol KL, Hamm P. Intrinsic phasing of heterodyne-detected multidimensional infrared spectra. OPTICS EXPRESS 2017; 25:2928-2938. [PMID: 29519009 DOI: 10.1364/oe.25.002928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We show that it is possible to phase multidimensional infrared spectra generated by a boxcars geometry four-wave mixing spectrometer directly from the signal generated by the molecular vibration of interest, without the need for auxiliary phasing measurements. For isolated vibrations, the phase profile of the 2D response smoothly varies between fixed phase limits, allowing for a general target for phasing independent of the degree of anharmonicity exhibited between the ground and excited state. As a proof of principle, the 2D response of the ∼2155 cm-1 thiocyanate stretch vibration of MeSCN, a system exhibiting anharmonicity such that the 0-1 and 1-2 transitions are spectrally isolated, is successfuly phased directly from the experimental spectra. The methodology is also applied to correctly phase extremely weak signals of the unnatural amino acid azidohomoalanine following background subtraction.
Collapse
|
26
|
Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
27
|
Mori T, Saito S. Molecular Mechanism Behind the Fast Folding/Unfolding Transitions of Villin Headpiece Subdomain: Hierarchy and Heterogeneity. J Phys Chem B 2016; 120:11683-11691. [DOI: 10.1021/acs.jpcb.6b08066] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| |
Collapse
|
28
|
Gosavi PM, Korendovych IV. Minimalist IR and fluorescence probes of protein function. Curr Opin Chem Biol 2016; 34:103-109. [PMID: 27599185 DOI: 10.1016/j.cbpa.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 11/19/2022]
Abstract
Spectroscopic studies of small proteins and peptides, especially those requiring fine spatial and/or temporal resolution, demand synthetic probes that confer the minimal possible steric and functional change on the native properties. Here we review the recent progress in development of minimally disruptive probes for fluorescence and infrared spectroscopies, as well as the methods to efficiently incorporate them into proteins. Advances in spectroscopy on the one hand result in high specialization of synthetic probes for a particular purpose, but on the other hand allow for the same probes be used for different techniques to gather complementary biochemical information.
Collapse
Affiliation(s)
- Pallavi M Gosavi
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States.
| |
Collapse
|
29
|
Hsu WL, Shih TC, Horng JC. Folding stability modulation of the villin headpiece helical subdomain by 4-fluorophenylalanine and 4-methylphenylalanine. Biopolymers 2016; 103:627-37. [PMID: 26017817 DOI: 10.1002/bip.22689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/25/2015] [Accepted: 05/25/2015] [Indexed: 11/10/2022]
Abstract
HP36, the helical subdomain of villin headpiece, contains a hydrophobic core composed of three phenylalanine residues (Phe47, Phe51, and Phe58). Hydrophobic effects and electrostatic interactions were shown to be the critical factors in stabilizing this core and the global structure. To assess the interactions among Phe47, Phe51, and Phe58 residues and investigate how they affect the folding stability, we implanted 4-fluorophenylalanine (Z) and 4-methylphenylalanine (X) into the hydrophobic core of HP36. We chemically synthesized HP36 and its seven variants including four single mutants whose Phe51 or Phe58 was replaced with Z or X, and three double mutants whose Phe51 and Phe58 were both substituted. Circular dichroism and nuclear magnetic resonance measurements show that the variants exhibit a native HP36 like fold, of which F51Z and three double mutants are more stable than the wild type. Molecular modeling provided detailed interaction energy within the phenylalanine residues, revealing that electrostatic interactions dominate the stability modulation upon the introduction of 4-fluorophenylalanine and 4-methylphenylalanine. Our results show that these two non-natural amino acids can successfully tune the interactions in a relatively compact hydrophobic core and the folding stability without inducing dramatic steric effects. Such an approach may be applied to other folded motifs or proteins.
Collapse
Affiliation(s)
- Wei-Lin Hsu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, 30013, R.O.C
| | - Ting-Chia Shih
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, 30013, R.O.C
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, 30013, R.O.C.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan, 30013, R.O.C
| |
Collapse
|
30
|
van Wilderen LJGW, Bredenbeck J. Von ultraschnellen Strukturbestimmungen bis zum Steuern von Reaktionen: mehrdimensionale gemischte IR/nicht-IR-Schwingungsspektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
31
|
van Wilderen LJGW, Bredenbeck J. From Ultrafast Structure Determination to Steering Reactions: Mixed IR/Non-IR Multidimensional Vibrational Spectroscopies. Angew Chem Int Ed Engl 2015; 54:11624-40. [PMID: 26394274 DOI: 10.1002/anie.201503155] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 12/27/2022]
Abstract
Ultrafast multidimensional infrared spectroscopy is a powerful method for resolving features of molecular structure and dynamics that are difficult or impossible to address with linear spectroscopy. Augmenting the IR pulse sequences by resonant or nonresonant UV, Vis, or NIR pulses considerably extends the range of application and creates techniques with possibilities far beyond a pure multidimensional IR experiment. These include surface-specific 2D-IR spectroscopy with sub-monolayer sensitivity, ultrafast structure determination in non-equilibrium systems, triggered exchange spectroscopy to correlate reactant and product bands, exploring the interplay of electronic and nuclear degrees of freedom, investigation of interactions between Raman- and IR-active modes, imaging with chemical contrast, sub-ensemble-selective photochemistry, and even steering a reaction by selective IR excitation. We give an overview of useful mixed IR/non-IR pulse sequences, discuss their differences, and illustrate their application potential.
Collapse
Affiliation(s)
| | - Jens Bredenbeck
- Institute of Biophysics, Johann Wolfgang Goethe-University, Frankfurt am Main (Germany).
| |
Collapse
|
32
|
Abstract
Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.
Collapse
Affiliation(s)
- Amanda L Le Sueur
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405, USA.
| | | | | |
Collapse
|
33
|
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.
Collapse
Affiliation(s)
| | | | - Feng Gai
- To whom correspondence should be addressed; ; Phone: 215-573-6256; Fax: 215-573-2112
| |
Collapse
|
34
|
Cai K, Du F, Liu J, Su T. Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:701-710. [PMID: 25260065 DOI: 10.1016/j.saa.2014.08.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/05/2014] [Accepted: 08/24/2014] [Indexed: 06/03/2023]
Abstract
The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the CO bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.
Collapse
Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China.
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| | - Jia Liu
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| | - Tingting Su
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| |
Collapse
|
35
|
Liu H, Lantz R, Cosme P, Rivera N, Andino C, Gonzalez WG, Terentis AC, Wojcikiewicz EP, Oyola R, Miksovska J, Du D. Site-specific dynamics of amyloid formation and fibrillar configuration of Aβ1–23 using an unnatural amino acid. Chem Commun (Camb) 2015; 51:7000-3. [DOI: 10.1039/c5cc00149h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Distinct local dynamics of Aβ1–23 amyloid formation are characterized using an unnatural amino acid p-cyanophenylalanine as a spectroscopic probe.
Collapse
Affiliation(s)
- Haiyang Liu
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | - Richard Lantz
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | - Patrick Cosme
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | - Nelson Rivera
- Department of Chemistry
- University of Puerto Rico-Humacao
- Humacao
- Puerto Rico
| | - Carlos Andino
- Department of Chemistry
- University of Puerto Rico-Humacao
- Humacao
- Puerto Rico
| | - Walter G. Gonzalez
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | - Andrew C. Terentis
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | | | - Rolando Oyola
- Department of Chemistry
- University of Puerto Rico-Humacao
- Humacao
- Puerto Rico
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | - Deguo Du
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| |
Collapse
|
36
|
Panek PT, Jacob CR. Efficient calculation of anharmonic vibrational spectra of large molecules with localized modes. Chemphyschem 2014; 15:3365-77. [PMID: 25080397 DOI: 10.1002/cphc.201402251] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Indexed: 11/11/2022]
Abstract
The analysis and interpretation of the vibrational spectra of complex (bio)molecular systems, such as polypeptides and proteins, requires support from quantum-chemical calculations. Such calculations are currently restricted to the harmonic approximation. Here, we show how one of the main bottlenecks in such calculations, the evaluation of the potential energy surface, can be overcome by using localized modes instead of the commonly employed normal modes. We apply such local vibrational self-consistent field (L-VSCF) and vibrational configuration interaction (L-VCI) calculations to a cyclic water tetramer and a helical hexa-alanine peptide. The results show that the use of localized modes is equivalent to the commonly used normal modes, but offers several advantages. First, a faster convergence with respect to the excitation level is observed in L-VCI calculations. Second, the localized modes provide a reduced representation of the couplings between modes that show a regular coupling pattern. This can be used to disregard a significant number of small two-mode potentials a priori. Several such reduced coupling approximations are explored, and we show that the number of single-point calculations required to evaluate the potential energy surface can be significantly reduced without introducing noticeable errors in the resulting vibrational spectra.
Collapse
Affiliation(s)
- Paweł T Panek
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures and Institute of Physical Chemistry, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe (Germany) http://www.christophjacob.eu
| | | |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Microscopic insights into the protein-stabilizing effect of trimethylamine N-oxide (TMAO). Proc Natl Acad Sci U S A 2014; 111:8476-81. [PMID: 24912147 DOI: 10.1073/pnas.1403224111] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Although it is widely known that trimethylamine N-oxide (TMAO), an osmolyte used by nature, stabilizes the folded state of proteins, the underlying mechanism of action is not entirely understood. To gain further insight into this important biological phenomenon, we use the C≡N stretching vibration of an unnatural amino acid, p-cyano-phenylalanine, to directly probe how TMAO affects the hydration and conformational dynamics of a model peptide and a small protein. By assessing how the lineshape and spectral diffusion properties of this vibration change with cosolvent conditions, we are able to show that TMAO achieves its protein-stabilizing ability through the combination of (at least) two mechanisms: (i) It decreases the hydrogen bonding ability of water and hence the stability of the unfolded state, and (ii) it acts as a molecular crowder, as suggested by a recent computational study, that can increase the stability of the folded state via the excluded volume effect.
Collapse
|
39
|
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. [DOI: 10.1002/ange.201402011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
40
|
Adhikary R, Zimmermann J, Dawson PE, Romesberg FE. IR Probes of Protein Microenvironments: Utility and Potential for Perturbation. Chemphyschem 2014; 15:849-53. [DOI: 10.1002/cphc.201400017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Indexed: 11/10/2022]
|
41
|
Gerace M, Loring RF. Two-dimensional spectroscopy of coupled vibrations with the optimized mean-trajectory approximation. J Phys Chem B 2013; 117:15452-61. [PMID: 23924378 PMCID: PMC3865215 DOI: 10.1021/jp405225g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The optimized mean-trajectory (OMT) approximation is a semiclassical representation of the nonlinear vibrational response function used to compute multidimensional infrared spectra. In this method, response functions are calculated from a sequence of classical trajectories linked by discontinuities representing the effects of radiation-matter interactions, thus providing an approximation to quantum dynamics using classical inputs. This approach was previously formulated and assessed numerically for a single anharmonic degree of freedom. Our previous work is generalized here in two respects. First, the derivation of the OMT is extended to any number of coupled anharmonic vibrations by determining semiclassical approximations for pairs of double-sided Feynman diagrams. Second, an efficient numerical procedure is developed for calculating two-dimensional infrared spectra of coupled anharmonic vibrations in the OMT approximation. The OMT approximation is shown to reproduce the fundamental features of the quantum response function including both coherence and population dynamics.
Collapse
Affiliation(s)
- Mallory Gerace
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York, 14853, USA
| | - Roger F. Loring
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York, 14853, USA
| |
Collapse
|
42
|
Gerace M, Loring RF. An optimized semiclassical approximation for vibrational response functions. J Chem Phys 2013; 138:124104. [PMID: 23556706 DOI: 10.1063/1.4795941] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The observables of multidimensional infrared spectroscopy may be calculated from nonlinear vibrational response functions. Fully quantum dynamical calculations of vibrational response functions are generally impractical, while completely classical calculations are qualitatively incorrect at long times. These challenges motivate the development of semiclassical approximations to quantum mechanics, which use classical mechanical information to reconstruct quantum effects. The mean-trajectory (MT) approximation is a semiclassical approach to quantum vibrational response functions employing classical trajectories linked by deterministic transitions representing the effects of the radiation-matter interaction. Previous application of the MT approximation to the third-order response function R(3)(t3, t2, t1) demonstrated that the method quantitatively describes the coherence dynamics of the t3 and t1 evolution times, but is qualitatively incorrect for the waiting-time t2 period. Here we develop an optimized version of the MT approximation by elucidating the connection between this semiclassical approach and the double-sided Feynman diagrams (2FD) that represent the quantum response. Establishing the direct connection between 2FD and semiclassical paths motivates a systematic derivation of an optimized MT approximation (OMT). The OMT uses classical mechanical inputs to accurately reproduce quantum dynamics associated with all three propagation times of the third-order vibrational response function.
Collapse
Affiliation(s)
- Mallory Gerace
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
| | | |
Collapse
|
43
|
Roy S, Bagchi B. Chemical Unfolding of Chicken Villin Headpiece in Aqueous Dimethyl Sulfoxide Solution: Cosolvent Concentration Dependence, Pathway, and Microscopic Mechanism. J Phys Chem B 2012; 117:4488-502. [DOI: 10.1021/jp308589b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Susmita Roy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore
560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore
560012, India
| |
Collapse
|
44
|
Chung JK, Thielges MC, Lynch SR, Fayer MD. Fast dynamics of HP35 for folded and urea-unfolded conditions. J Phys Chem B 2012; 116:11024-31. [PMID: 22909017 DOI: 10.1021/jp304058x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The changes in fast dynamics of HP35 with a double CN vibrational dynamics label (HP35-P(2)) as a function of the extent of denaturation by urea were investigated with two-dimensional infrared (2D IR) vibrational echo spectroscopy. Cyanophenylalanine (PheCN) replaces the native phenylalanine at two residues in the hydrophobic core of HP35, providing vibrational probes. NMR data show that HP35-P(2) maintains the native folded structure similar to wild type and that both PheCN residues share essentially the same environment within the peptide. A series of time-dependent 2D IR vibrational echo spectra were obtained for the folded peptide and the increasingly unfolded peptide. Analysis of the time dependence of the 2D spectra yields the system's spectral diffusion, which is caused by the sampling of accessible structures of the peptide under thermal equilibrium conditions. The structural dynamics become faster as the degree of unfolding is increased.
Collapse
Affiliation(s)
- Jean K Chung
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | | | | |
Collapse
|
45
|
Wang L, Skinner JL. Thermally induced protein unfolding probed by isotope-edited IR spectroscopy. J Phys Chem B 2012; 116:9627-34. [PMID: 22853174 PMCID: PMC3463243 DOI: 10.1021/jp304613b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Infrared (IR) spectroscopy has been widely utilized for the study of protein folding, unfolding, and misfolding processes. We have previously developed a theoretical method for calculating IR spectra of proteins in the amide I region. In this work, we apply this method, in combination with replica-exchange molecular dynamics simulations, to study the equilibrium thermal unfolding transition of the villin headpiece subdomain (HP36). Temperature-dependent IR spectra and spectral densities are calculated. The spectral densities correctly reflect the unfolding conformational changes in the simulation. With the help of isotope labeling, we are able to capture the feature that helix 2 of HP36 loses its secondary structure before global unfolding occurs, in agreement with experiment.
Collapse
Affiliation(s)
- Lu Wang
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706 USA
| | - James L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706 USA
| |
Collapse
|