1
|
Maiti KS. Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein. Molecules 2021; 26:molecules26226893. [PMID: 34833985 PMCID: PMC8618531 DOI: 10.3390/molecules26226893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022] Open
Abstract
Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.
Collapse
Affiliation(s)
- Kiran Sankar Maiti
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; ; Tel.: +49-89-289-54056
- Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Coulombwall 1, 85748 Garching, Germany
| |
Collapse
|
2
|
Volk M, Milanesi L, Waltho JP, Hunter CA, Beddard GS. The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone. Phys Chem Chem Phys 2015; 17:762-82. [DOI: 10.1039/c4cp03058c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recombination of photolysed protein disulfide bonds confirms subdiffusional backbone motion and measures the roughness of the protein's energy landscape.
Collapse
Affiliation(s)
- Martin Volk
- Department of Chemistry
- University of Liverpool
- Liverpool
- UK
| | - Lilia Milanesi
- School of Chemical and Biological Sciences
- Queen Mary
- University of London
- London
- UK
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology
- University of Sheffield
- Sheffield
- UK
- Manchester Institute of Biotechnology
| | | | | |
Collapse
|
3
|
Courter JR, Abdo M, Brown SP, Tucker MJ, Hochstrasser RM, Smith AB. The design and synthesis of alanine-rich α-helical peptides constrained by an S,S-tetrazine photochemical trigger: a fragment union approach. J Org Chem 2013; 79:759-68. [PMID: 24359446 DOI: 10.1021/jo402680v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The design and synthesis of alanine-rich α-helical peptides constrained in a partially unfolded state by incorporation of the S,S-tetrazine phototrigger has been achieved, permitting, upon photochemical release, observation by 2D-IR spectroscopy of the subnanosecond conformational dynamics that govern the early steps associated with α-helix formation. Solid-phase peptide synthesis was employed to elaborate the requisite fragments, with full peptide construction via solution-phase fragment condensation. The fragment union tactic was also employed to construct (13)C═(18)O isotopically edited amides to permit direct observation of conformational motion at or near specific peptide bonds.
Collapse
Affiliation(s)
- Joel R Courter
- Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | | | | | | | | | | |
Collapse
|
4
|
Gregory MJ, Anderson M, Causgrove TP. Measurement of energy barriers to conformational change in poly-l-glutamic acid by temperature-derivative spectroscopy. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
5
|
Jiao T, Gao L, Chen X, Fang W. The Folding Dynamics and Infrared Spectra of a Photocleaved Tetrapeptide Predicted by Theoretical Simulations. J Phys Chem B 2012. [DOI: 10.1021/jp311286k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tiantian Jiao
- Key Laboratory of Theoretical and
Computational Photochemistry,
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lianghui Gao
- Key Laboratory of Theoretical and
Computational Photochemistry,
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xuebo Chen
- Key Laboratory of Theoretical and
Computational Photochemistry,
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Weihai Fang
- Key Laboratory of Theoretical and
Computational Photochemistry,
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
6
|
Milanesi L, Waltho JP, Hunter CA, Shaw DJ, Beddard GS, Reid GD, Dev S, Volk M. Measurement of energy landscape roughness of folded and unfolded proteins. Proc Natl Acad Sci U S A 2012; 109:19563-8. [PMID: 23150572 PMCID: PMC3511724 DOI: 10.1073/pnas.1211764109] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dynamics of protein conformational changes, from protein folding to smaller changes, such as those involved in ligand binding, are governed by the properties of the conformational energy landscape. Different techniques have been used to follow the motion of a protein over this landscape and thus quantify its properties. However, these techniques often are limited to short timescales and low-energy conformations. Here, we describe a general approach that overcomes these limitations. Starting from a nonnative conformation held by an aromatic disulfide bond, we use time-resolved spectroscopy to observe nonequilibrium backbone dynamics over nine orders of magnitude in time, from picoseconds to milliseconds, after photolysis of the disulfide bond. We find that the reencounter probability of residues that initially are in close contact decreases with time following an unusual power law that persists over the full time range and is independent of the primary sequence. Model simulations show that this power law arises from subdiffusional motion, indicating a wide distribution of trapping times in local minima of the energy landscape, and enable us to quantify the roughness of the energy landscape (4-5 k(B)T). Surprisingly, even under denaturing conditions, the energy landscape remains highly rugged with deep traps (>20 k(B)T) that result from multiple nonnative interactions and are sufficient for trapping on the millisecond timescale. Finally, we suggest that the subdiffusional motion of the protein backbone found here may promote rapid folding of proteins with low contact order by enhancing contact formation between nearby residues.
Collapse
Affiliation(s)
- Lilia Milanesi
- Departments of Molecular Biology and Biotechnology and
- Chemistry, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Jonathan P. Waltho
- Departments of Molecular Biology and Biotechnology and
- Manchester Institute of Biotechnology, Manchester M1 7DN, United Kingdom
| | | | - Daniel J. Shaw
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; and
| | - Godfrey S. Beddard
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; and
| | - Gavin D. Reid
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; and
| | - Sagarika Dev
- Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Martin Volk
- Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| |
Collapse
|
7
|
Abdo M, Brown SP, Courter JR, Tucker MJ, Hochstrasser RM, Smith AB. Design, synthesis, and photochemical validation of peptide linchpins containing the S,S-tetrazine phototrigger. Org Lett 2012; 14:3518-21. [PMID: 22731895 DOI: 10.1021/ol301490h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The design, solid-phase synthesis, and photochemical validation of diverse peptide linchpins, containing the S,S-tetrazine phototrigger, have been achieved. Steady state irradiation or femtosecond laser pulses confirm their rapid photofragmentation. Attachment of peptides to the C- and N-termini will provide access to diverse constrained peptide constructs that hold the promise of providing information about early peptide/protein conformational dynamics upon photochemical release.
Collapse
Affiliation(s)
- Mohannad Abdo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | | | |
Collapse
|
8
|
Buchner GS, Murphy RD, Buchete NV, Kubelka J. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1001-20. [PMID: 20883829 DOI: 10.1016/j.bbapap.2010.09.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 09/14/2010] [Accepted: 09/16/2010] [Indexed: 10/19/2022]
Abstract
The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at multiple levels, from atomistic to coarse-grained representations. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
Collapse
Affiliation(s)
- Ginka S Buchner
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA; Universität Würzbug, Würzburg, Germany
| | | | | | | |
Collapse
|
9
|
Hache F. Application of time-resolved circular dichroism to the study of conformational changes in photochemical and photobiological processes. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2009.03.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
10
|
Milanesi L, Jelinska C, Hunter CA, Hounslow AM, Staniforth RA, Waltho JP. A Method for the Reversible Trapping of Proteins in Non-Native Conformations. Biochemistry 2008; 47:13620-34. [DOI: 10.1021/bi801362f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lilia Milanesi
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Clare Jelinska
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Christopher A. Hunter
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Andrea M. Hounslow
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Rosemary A. Staniforth
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| |
Collapse
|
11
|
Hobley J, Kuge Y, Gorelik S, Kasuya M, Hatanaka K, Kajimoto S, Fukumura H. Water expansion dynamics after pulsed IR laser heating. Phys Chem Chem Phys 2008; 10:5256-63. [DOI: 10.1039/b805838e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
12
|
Schadendorf T, Hoppmann C, Rück-Braun K. Synthesis of rigid photoswitchable hemithioindigo ω-amino acids. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.10.110] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
13
|
Kolano C, Helbing J, Bucher G, Sander W, Hamm P. Intramolecular Disulfide Bridges as a Phototrigger To Monitor the Dynamics of Small Cyclic Peptides. J Phys Chem B 2007; 111:11297-302. [PMID: 17764169 DOI: 10.1021/jp074184g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two cyclic disulfide-bridged tetrapeptides [cyclo(Boc-Cys-Pro-Aib-Cys-OMe) (1) and cyclo(Boc-Cys-Pro-Phe-Cys-OMe) (2)] have been monitored by time-resolved mid-IR spectroscopy in the C=O vibrational range. A conformational change is induced by cleavage of the intramolecular disulfide bridge upon UV excitation (lambda(exc) = 260 nm), giving rise to a pair of cysteinyl radicals (thiyl radicals), which diffuse apart allowing the peptide to change conformation before they undergo quenching. The amide I band reports on the dynamics of the peptide backbone, which evolves on a 100 ps time scale and then stays constant up to 10 micros at low enough concentrations ( approximately 100 mM). To probe specifically the lifetime of the free cysteinyl radicals, time-resolved UV laser flash photolysis has been applied. The concentration of the cysteinyl radical decays nonexponentially, but about 50% are still present after 1 ms. The photocleavable disulfide bridge hence may serve as an intrinsic, naturally occurring phototrigger to study peptide dynamics that opens a wide time-window from a few picoseconds to many hundreds of microseconds.
Collapse
Affiliation(s)
- Christoph Kolano
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
| | | | | | | | | |
Collapse
|
14
|
Kay ER, Leigh DA, Zerbetto F. Synthetic molecular motors and mechanical machines. Angew Chem Int Ed Engl 2007; 46:72-191. [PMID: 17133632 DOI: 10.1002/anie.200504313] [Citation(s) in RCA: 2044] [Impact Index Per Article: 120.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.
Collapse
Affiliation(s)
- Euan R Kay
- School of Chemistry, University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK
| | | | | |
Collapse
|
15
|
Kay E, Leigh D, Zerbetto F. Synthetische molekulare Motoren und mechanische Maschinen. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200504313] [Citation(s) in RCA: 587] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
16
|
Abstract
The photoinduced isomerization of azobenzene between the extended (trans) and compact (cis) conformations is reversibly triggered by light of two differing wavelengths. The resulting changes in molecular geometry have been extensively utilized to photoswitch transformations in chemical species reversibly for applications in optoelectronic devises as well as to photocontrol conformational states in (bio)polymers. The high isomerization yield, remarkable photostability and ultrafast kinetics (few ps) of azobenzene are well suited for the design of small, defined model systems that allow detailed folding studies to be carried out both experimentally and theoretically on the same molecules. In our and other laboratories such systems were recently obtained with cyclic peptides of defined conformational preferences as well as with alpha-helical and beta-hairpin peptides. These should, by comparison of simulation and experiment, permit an assessment and improvement of the theoretical description on the one hand and a detailed interpretation of the ultrafast conformational dynamics on the other. The phototriggered changes in conformational states lead to concurrent changes in biophysical properties that can be exploited in the photocontrol of biochemical and biological events, as exemplarily discussed with redox-active cyclic bis-cysteinyl peptides and receptor ligands.
Collapse
Affiliation(s)
- Christian Renner
- School of Biomedical and Natural Sciences, Nottingham Trent University, Nottingham, NG11 8NS, UK.
| | | |
Collapse
|
17
|
Nguyen PH, Gorbunov RD, Stock G. Photoinduced conformational dynamics of a photoswitchable peptide: a nonequilibrium molecular dynamics simulation study. Biophys J 2006; 91:1224-34. [PMID: 16731560 PMCID: PMC1518633 DOI: 10.1529/biophysj.106.084996] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Employing nonequilibrium molecular dynamics simulations, a comprehensive computational study of the photoinduced conformational dynamics of a photoswitchable bicyclic azobenzene octapeptide is presented. The calculation of time-dependent probability distributions along various global and local reaction coordinates reveals that the conformational rearrangement of the peptide is rather complex and occurs on at least four timescales: 1) After photoexcitation, the azobenzene unit of the molecule undergoes nonadiabatic photoisomerization within 0.2 ps. 2) On the picosecond timescale, the cooling (13 ps) and the stretching (14 ps) of the photoexcited peptide is observed. 3) Most reaction coordinates exhibit a 50-100 ps component reflecting a fast conformational rearrangement. 4) The 500-1000 ps component observed in the simulation accounts for the slow diffusion-controlled conformational equilibration of the system. The simulation of the photoinduced molecular processes is in remarkable agreement with time-resolved optical and infrared experiments, although the calculated cooling as well as the initial conformational rearrangements of the peptide appear to be somewhat too slow. Based on an ab initio parameterized vibrational Hamiltonian, the time-dependent amide I frequency shift is calculated. Both intramolecular and solvent-induced contributions to the frequency shift were found to change by < or = 2 cm(-1), in reasonable agreement with experiment. The potential of transient infrared spectra to characterize the conformational dynamics of peptides is discussed in some detail.
Collapse
Affiliation(s)
- Phuong H Nguyen
- Institute of Physical and Theoretical Chemistry, J. W. Goethe University, Frankfurt, Germany
| | | | | |
Collapse
|
18
|
Pozo Ramajo A, Petty SA, Volk M. Fast folding dynamics of α-helical peptides – Effect of solvent additives and pH. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.08.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
19
|
Reducing the vibrational coupling network in N-methylacetamide as a model for ab initio infrared spectra computations of peptides. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.08.037] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
20
|
|
21
|
Löweneck M, Milbradt AG, Root C, Satzger H, Zinth W, Moroder L, Renner C. A conformational two-state peptide model system containing an ultrafast but soft light switch. Biophys J 2005; 90:2099-108. [PMID: 16387780 PMCID: PMC1386788 DOI: 10.1529/biophysj.105.067363] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Combining an azobenzene chromophore with the bis-cysteinyl active-site sequence of the protein disulfide isomerase (PDI) we constructed a simple but promising model for allosteric conformational rearrangements. Paralleling cellular signaling events, an external trigger, here absorption of a photon, leads to a structural change in one part of the molecule, namely the azobenzene-based chromophore. The change in geometry translates to the effector site, in our case the peptide sequence, where it modifies covalent and nonbonded interactions and thus leads to a conformational rearrangement. NMR spectroscopy showed that the trans-azo and cis-azo isomer of the cyclic PDI peptide exhibit different, but well-defined structures when the two cystine residues form a disulfide bridge. Without this intramolecular cross-link conformationally more variable structural ensembles are obtained that again differ for the two isomeric states. Ultrafast UV/Vis spectroscopy confirmed that the rapid isomerization of azobenzene is not significantly slowed down when incorporated into the cyclic peptides, although the amplitudes of ballistic and diffusive pathways are changed. The observation that most of the energy of an absorbed photon is dissipated to the solvent in the first few picoseconds when the actual azo-isomerization takes place is important. The conformational rearrangement is weakly driven due to the absence of appreciable excess energy and can be described as biased diffusion similar to natural processes.
Collapse
Affiliation(s)
- Markus Löweneck
- Max-Planck-Institut für Biochemie, 82152 Martinsried, Germany
| | | | | | | | | | | | | |
Collapse
|
22
|
Nguyen PH, Mu Y, Stock G. Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study. Proteins 2005; 60:485-94. [PMID: 15977160 DOI: 10.1002/prot.20485] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A replica exchange molecular dynamics (REMD) simulation of a bicyclic azobenzene peptide in explicit dimethyl sulfoxide solution is presented in order to characterize the conformational structures and energy landscape of a photoswitchable peptide. It is shown that an enhanced-sampling technique such as the REMD method is essential to obtain a converged conformational sampling of the peptide at room temperature. This is because conventional MD simulations of less than approximately 100-ns length are either trapped in local minima (at 295 K) or-if run at high temperature-do not resemble the room-temperature REMD results. Calculating various nuclear Overhauser effects (NOEs) and (3)J-couplings, a good overall agreement between the REMD simulations and the NMR experiments of Renner et al. (Biopolymers 2000;54:501-514) is found. In particular, the REMD study confirms the general picture drawn by Renner et al. that the trans-isomer of the azobenzene peptide exhibits a well-defined structure, while the cis-isomer is a conformational heterogeneous system; that is, the trans-isomer occurs in 2 well-defined conformers, while the cis-isomer represents an energetically frustrated system that leads to an ensemble of conformational structures. Employing a principal component analysis of the REMD data, the free energy landscape of the systems is studied at various temperatures. The implications for the folding and unfolding pathways of the system are discussed.
Collapse
Affiliation(s)
- Phuong H Nguyen
- Institute of Physical and Theoretical Chemistry, J. W. Goethe University, Frankfurt, Germany
| | | | | |
Collapse
|
23
|
Nölting B, Schälike W, Hampel P, Grundig F, Gantert S, Sips N, Bandlow W, Qi PX. Structural determinants of the rate of protein folding. J Theor Biol 2003; 223:299-307. [PMID: 12850450 DOI: 10.1016/s0022-5193(03)00091-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To understand the mechanism of protein folding and to assist rational design of fast-folding, non-aggregating and stable artificial enzymes, it is essential to determine the structural parameters which govern the rate constants of folding, kf. It has been found that -logkf is a linear function of the so-called chain topology parameter (CTP) within the range of 10(-1)s(-1)< or = kf < or =10(8)s(-1). The correlation between -logkf and CTP is much improved than using previously published contact order (CO) method. It has been further suggested that short sequence separations may be preferred for the establishment of stable interactions for the design of novel artificial enzymes and the modification of slow-folding proteins with aggregating intermediates.
Collapse
Affiliation(s)
- Bengt Nölting
- Prussian Private Institute of Technology at Berlin, Am Schlosspark 30, Berlin D-13187, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Bredenbeck J, Helbing J, Sieg A, Schrader T, Zinth W, Renner C, Behrendt R, Moroder L, Wachtveitl J, Hamm P. Picosecond conformational transition and equilibration of a cyclic peptide. Proc Natl Acad Sci U S A 2003; 100:6452-7. [PMID: 12736378 PMCID: PMC164467 DOI: 10.1073/pnas.1036583100] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ultrafast IR spectroscopy is used to monitor the nonequilibrium backbone dynamics of a cyclic peptide in the amide I vibrational range with picosecond time resolution. A conformational change is induced by means of a photoswitch integrated into the peptide backbone. Although the main conformational change of the backbone is completed after only 20 ps, the subsequent equilibration in the new region of conformational space continues for times >16 ns. Relaxation and equilibration processes of the peptide backbone occur on a discrete hierarchy of time scales. Albeit possessing only a few conformational degrees of freedom compared with a protein, the peptide behaves highly nontrivially and provides insights into the complexity of fast protein folding.
Collapse
Affiliation(s)
- Jens Bredenbeck
- Universität Zürich, Physikalisch Chemisches Institut, Winterthurer Strasse 190, Switzerland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Biris N, Stavrakoudis A, Politou AS, Mikros E, Sakarellos-Daitsiotis M, Sakarellos C, Tsikaris V. The Ac-RGD-NH2 peptide as a probe of slow conformational exchange of short linear peptides in DMSO. Biopolymers 2003; 69:72-86. [PMID: 12717723 DOI: 10.1002/bip.10335] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
According to general belief, the conformational information on short linear peptides in solution derived at ambient temperature from NMR spectrometry represents a population-weighted average over all members of an ensemble of rapidly interconverting conformations. Usually the search for discrete conformations is concentrated at low temperatures especially when sharp NMR resonances are detected at room temperature. Using the peptide Ac-RGD-NH(2) (Ac-Arg-Gly-Asp-NH(2), Ac: acetyl) as a model system and following a new approach, we have been able to demonstrate that short linear peptides can adopt discrete conformational states in DMSO-d(6) (DMSO: dimethylsulfoxide) which vary in a way critically dependent on the reconstitution conditions used before their dissolution in DMSO-d(6). The conformers are stabilized by intramolecular hydrogen bonds, which persist at high temperatures and undergo a very slow exchange with their extended structures in the NMR chemical shift time scale. The reported findings provide clear evidence for the occurrence of solvent-induced conformational exchange and point to DMSO as a valuable medium for folding studies of short linear peptides.
Collapse
|
26
|
Abstract
Although analysis strategies exist for probing a diverse array of molecular properties, most of these approaches are not amenable to the study of reaction intermediates and other transient species. Separations in particular can provide detailed information on attributes not readily measured by spectroscopy but typically are performed over time scales much longer than the life span of highly unstable compounds. Here we report the development of an electrophoretic strategy that dramatically extends the practical speed limit for fractionations and demonstrate its utility in examining transient hydroxyindole photoproducts. Fluorescent reaction intermediates are optically generated in femtoliter volumes within a flowing reagent stream and are differentially transported at velocities as large as 1.3 m.s(-1), thereby minimizing band variance and allowing multicomponent reaction mixtures to be resolved over separation paths as short as 9 microm. Analyte migration times and band variances do not deviate significantly from basic theory for separations performed with fields that exceed 0.1 MV.cm(-1), indicating that effects from Joule heating are minor. We demonstrate the feasibility of achieving baseline resolution of a binary mixture in <10 micros, nearly 100-fold faster than previously possible. Application of this approach to the study of a range of short-lived molecules should be feasible.
Collapse
Affiliation(s)
- Matthew L Plenert
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology and the Center for Nano- and Molecular Science and Engineering, University of Texas, Austin, TX 78712, USA
| | | |
Collapse
|
27
|
Lapidus LJ, Eaton WA, Hofrichter J. Measuring dynamic flexibility of the coil state of a helix-forming peptide. J Mol Biol 2002; 319:19-25. [PMID: 12051933 DOI: 10.1016/s0022-2836(02)00193-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
To investigate the dynamic flexibility of the coil state of a helix-forming peptide the end-to-end contact rate was determined. Nanosecond optical excitation of tryptophan at one end of a 22 residue, alanine peptide populates a long-lived triplet state which is quenched upon close contact with a cyclic disulfide attached to the opposite end. Analysis of the decay of the triplet population using a two-state model for helix formation yields the diffusion-limited end-to-end contact rate of the coil state of the peptide as well as the helix-->coil and coil-->helix rates. The helix-coil rates are very similar to those previously measured in laser temperature-jump experiments. The end-to-end contact rate of 1.1 x 10(7) s(-1) in the coil state is tenfold faster than the rate for a disordered peptide with threonine substituted for alanine and, somewhat surprisingly, is about twice the rate for a disordered glycine-containing peptide. These differences are discussed in terms of the theory of Szabo, Schulten and Schulten. The rates should provide important new benchmarks for testing the accuracy of atomistic molecular dynamics simulations.
Collapse
Affiliation(s)
- Lisa J Lapidus
- Laboratory of Chemical Physics, Building 5, 5 Center Drive, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | | | | |
Collapse
|