1
|
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
|
2
|
Kim C, Kim Y, Lee SJ, Yun SR, Choi J, Kim SO, Yang Y, Ihee H. Visualizing Heterogeneous Protein Conformations with Multi-Tilt Nanoparticle-Aided Cryo-Electron Microscopy Sampling. NANO LETTERS 2023; 23:3334-3343. [PMID: 37068052 PMCID: PMC10141564 DOI: 10.1021/acs.nanolett.3c00313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Obtaining the heterogeneous conformation of small proteins is important for understanding their biological role, but it is still challenging. Here, we developed a multi-tilt nanoparticle-aided cryo-electron microscopy sampling (MT-NACS) technique that enables the observation of heterogeneous conformations of small proteins and applied it to calmodulin. By imaging the proteins labeled by two gold nanoparticles at multiple tilt angles and analyzing the projected positions of the nanoparticles, the distributions of 3D interparticle distances were obtained. From the measured distance distributions, the conformational changes associated with Ca2+ binding and salt concentration were determined. MT-NACS was also used to track the structural change accompanied by the interaction between amyloid-beta and calmodulin, which has never been observed experimentally. This work offers an alternative platform for studying the functional flexibility of small proteins.
Collapse
Affiliation(s)
- Changin Kim
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Yeeun Kim
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
| | - Sang Jin Lee
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - So Ri Yun
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Jungkweon Choi
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seong Ok Kim
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Yongsoo Yang
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Y.Y.:
email, ; tel, +82-42-350-7303
| | - Hyotcherl Ihee
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
- H.I.: email, ; tel, +82-42-350-2844
| |
Collapse
|
3
|
Howe CP, Greetham GM, Procacci B, Parker AW, Hunt NT. Sequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy. J Phys Chem B 2023; 127:1586-1597. [PMID: 36787177 PMCID: PMC9969394 DOI: 10.1021/acs.jpcb.2c08709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Time-resolved temperature-jump/drop infrared (IR) spectroscopy has been used to measure the impact of stem base sequence on the melting and refolding dynamics of ribonucleic acid (RNA) tetraloops. A series of three 12-nucleotide RNA hairpin sequences were studied, each featuring a UACG tetraloop motif and a double-stranded stem containing four base pairs. In each case, the stem comprised three GC pairs plus a single AU base pair inserted at the closing point of the loop (RNAloop), in the middle of the stem (RNAmid), or at the stem terminus (RNAend). Results from analogous DNA tetraloop (TACG) sequences were also obtained. Inclusion of AU or AT base pairs in the stem leads to faster melting of the stem-loop structure compared to a stem sequence featuring four GC base pairs while refolding times were found to be slower, consistent with a general reduction in stem-loop stability caused by the AU/AT pair. Independent measurement of the dynamic timescales for melting and refolding of ring vibrational modes of guanine (GR) and adenine (AR) provided position-specific insight into hairpin dynamics. The GR-derived data showed that DNA sequences melted more quickly (0.5 ± 0.1 to 0.7 ± 0.1 μs at 70 °C) than analogous RNA sequences (4.3 ± 0.4 to 4.4 ± 0.3 μs at 70 °C). Position-sensitive data from the AR modes suggests that DNA hairpins begin melting from the terminal end of the stem toward the loop while RNA sequences begin melting from the loop. Refolding timescales for both RNA and DNA hairpins were found to be similar (250 ± 50 μs at 70 °C) except for RNAend and DNAloop which refolded much more slowly (746 ± 36 and 430 ± 31 μs, respectively), showing that the refolding pathway is significantly impaired by the placement of AU/AT pairs at different points in the stem. We conclude that conformational changes of analogous pairs of RNA and DNA tetraloops proceed by different mechanisms.
Collapse
Affiliation(s)
- C P Howe
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - G M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, Oxon, U.K
| | - B Procacci
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - A W Parker
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, Oxon, U.K
| | - N T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| |
Collapse
|
4
|
Howe CP, Greetham GM, Procacci B, Parker AW, Hunt NT. Measuring RNA UNCG Tetraloop Refolding Dynamics Using Temperature-Jump/Drop Infrared Spectroscopy. J Phys Chem Lett 2022; 13:9171-9176. [PMID: 36166668 PMCID: PMC9549515 DOI: 10.1021/acs.jpclett.2c02338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Determining the structural dynamics of RNA and DNA is essential to understanding their cellular function, but direct measurement of strand association or folding remains experimentally challenging. Here we illustrate a temperature-jump/drop method able to reveal refolding dynamics. Time-resolved temperature-jump/drop infrared spectroscopy is used to measure the melting and refolding dynamics of a 12-nucleotide RNA sequence comprising a UACG tetraloop and a four-base-pair double-stranded GC stem, comparing them to an equivalent DNA (TACG) sequence. Stem-loop melting occurred an order of magnitude more slowly in RNA than DNA (6.0 ± 0.1 μs versus 0.8 ± 0.1 μs at 70 °C). In contrast, the refolding dynamics of both sequences occurred on similar time scales (200 μs). While the melting and refolding dynamics of RNA and DNA hairpins both followed Arrhenius temperature dependences, refolding was characterized by an apparent negative activation energy, consistent with a mechanism involving multiple misfolded intermediates prior to zipping of the stem base pairs.
Collapse
Affiliation(s)
- C. P. Howe
- Department
of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K.
| | - G. M. Greetham
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory,
Harwell Oxford, Didcot, Oxon OX11 0QX, U.K.
| | - B. Procacci
- Department
of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K.
| | - A. W. Parker
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory,
Harwell Oxford, Didcot, Oxon OX11 0QX, U.K.
| | - N. T. Hunt
- Department
of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K.
| |
Collapse
|
5
|
Liu S, Featherston ER, Cotruvo JA, Baiz CR. Lanthanide-dependent coordination interactions in lanmodulin: a 2D IR and molecular dynamics simulations study. Phys Chem Chem Phys 2021; 23:21690-21700. [PMID: 34581354 DOI: 10.1039/d1cp03628a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The biological importance of lanthanides, and the early lanthanides (La3+-Nd3+) in particular, has only recently been recognized, and the structural principles underlying selective binding of lanthanide ions in biology are not yet well established. Lanmodulin (LanM) is a novel protein that displays unprecedented affinity and selectivity for lanthanides over most other metal ions, with an uncommon preference for the early lanthanides. Its utilization of EF-hand motifs to bind lanthanides, rather than the Ca2+ typically recognized by these motifs in other proteins, has led it to be used as a model system to understand selective lanthanide recognition. Two-dimensional infrared (2D IR) spectroscopy combined with molecular dynamics simulations were used to investigate LanM's selectivity mechanisms by characterizing local binding site geometries upon coordination of early and late lanthanides as well as calcium. These studies focused on the protein's uniquely conserved proline residues in the second position of each EF-hand binding loop. We found that these prolines constrain the EF-hands for strong coordination of early lanthanides. Substitution of this proline results in a more flexible binding site to accommodate a larger range of ions but also results in less compact coordination geometries and greater disorder within the binding site. Finally, we identify the conserved glycine in the sixth position of each EF-hand as a mediator of local binding site conformation and global secondary structure. Uncovering fundamental structure-function relationships in LanM informs the development of synthetic biology technologies targeting lanthanides in industrial applications.
Collapse
Affiliation(s)
- Stephanie Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Emily R Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
6
|
Meech S. Virtual Issue on Ultrafast Spectroscopy. J Phys Chem B 2021; 125:6037-6039. [PMID: 34134490 DOI: 10.1021/acs.jpcb.1c04148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Steve Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, U.K
| |
Collapse
|
7
|
Edington SC, Liu S, Baiz CR. Infrared spectroscopy probes ion binding geometries. Methods Enzymol 2021; 651:157-191. [PMID: 33888203 DOI: 10.1016/bs.mie.2020.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.
Collapse
Affiliation(s)
- Sean C Edington
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Stephanie Liu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States.
| |
Collapse
|
8
|
Greetham GM, Clark IP, Young B, Fritsch R, Minnes L, Hunt NT, Towrie M. Time-Resolved Temperature-Jump Infrared Spectroscopy at a High Repetition Rate. APPLIED SPECTROSCOPY 2020; 74:720-727. [PMID: 32114769 DOI: 10.1177/0003702820913636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Time-resolved temperature-jump infrared absorption spectroscopy at a 0.5 to 1 kHz repetition rate is presented. A 1 kHz neodymium-doped yttrium aluminum garnet (Nd:YAG) laser pumping an optical parametric oscillator provided >70 µJ, 3.75 µm pump pulses, which delivered a temperature jump via excitation of the O-D stretch of a D2O solution. A 10 kHz train of mid-infrared probe pulses was used to monitor spectral changes following the temperature jump. Calibration with trifluoroacetic acid solution showed that a temperature jump of 10 K lasting for tens of microseconds was achieved, sufficient to observe fast processes in functionally relevant biomolecular mechanisms. Modeling of heating profiles across ≤10 µm path length cells and subsequent cooling dynamics are used to describe the initial <100 ns cooling at the window surface and subsequent, >10 µs cooling dynamics of the bulk solution.
Collapse
Affiliation(s)
- Gregory M Greetham
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, UK
| | - Ian P Clark
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, UK
| | - Benjamin Young
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, UK
| | - Robby Fritsch
- Department of Physics, SUPA, University of Strathclyde, Glasgow, UK
| | - Lucy Minnes
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, UK
- Department of Physics, SUPA, University of Strathclyde, Glasgow, UK
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York, UK
| | - Mike Towrie
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, UK
| |
Collapse
|