1
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Wang T, Yamato T, Sugiura W. Thermal Energy Transport through Nonbonded Native Contacts in Protein. J Phys Chem B 2024; 128:8641-8650. [PMID: 39197018 DOI: 10.1021/acs.jpcb.4c03475] [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: 08/30/2024]
Abstract
Within the protein interior, where we observe various types of interactions, nonuniform flow of thermal energy occurs along the polypeptide chain and through nonbonded native contacts, leading to inhomogeneous transport efficiencies from one site to another. The folded native protein serves not merely as thermal transfer medium but, more importantly, as sophisticated molecular nanomachines in cells. Therefore, we are particularly interested in what sort of "communication" is mediated through native contacts in the folded proteins and how such features are quantitatively depicted in terms of local transport coefficients of heat currents. To address the issue, we introduced a concept of inter-residue thermal conductivity and characterized the nonuniform thermal transport properties of a small globular protein, HP36, using equilibrium molecular dynamics simulation and the Green-Kubo formula. We observed that the thermal transport of the protein was dominated by that along the polypeptide chain, while the local thermal conductivity of nonbonded native contacts decreased in the order of H-bonding > π-stacking > electrostatic > hydrophobic contacts. Furthermore, we applied machine learning techniques to analyze the molecular mechanism of protein thermal transport. As a result, the contact distance, variance in contact distance, and H-bonding occurrence probability during MD simulations are found to be the top three important determinants for predicting local thermal transport coefficients.
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Affiliation(s)
- Tingting Wang
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takahisa Yamato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Wataru Sugiura
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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2
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Poudel H, Wales DJ, Leitner DM. Vibrational Energy Landscapes and Energy Flow in GPCRs. J Phys Chem B 2024; 128:7568-7576. [PMID: 39058920 DOI: 10.1021/acs.jpcb.4c04513] [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: 07/28/2024]
Abstract
We construct and analyze disconnectivity graphs to provide the first graphical representation of the vibrational energy landscape of a protein, in this study β2AR, a G-protein coupled receptor (GPCR), in active and inactive states. The graphs, which indicate the relative free energy of each residue and the minimum free energy barriers for energy transfer between them, reveal important composition, structural and dynamic properties that mediate the flow of energy. Prolines and glycines, which contribute to GPCR plasticity and function, are identified as bottlenecks to energy transport along the backbone from which alternative pathways for energy transport via nearby noncovalent contacts emerge, seen also in the analysis of first passage time (FPT) distributions presented here. Striking differences between the disconnectivity graphs and FPT distributions for the inactive and active states of β2AR are found where structural and dynamic changes occur upon activation, contributing to allosteric regulation.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - David J Wales
- Yusuf Hamied Department of Chemistry, Cambridge University, Cambridge CB2 1EW, U.K
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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3
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Feid C, Luma L, Fischer T, Löffler JG, Grebenovsky N, Wachtveitl J, Heckel A, Bredenbeck J. Iminothioindoxyl Donors with Exceptionally High Cross Section for Protein Vibrational Energy Transfer. Angew Chem Int Ed Engl 2024; 63:e202317047. [PMID: 38103205 DOI: 10.1002/anie.202317047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 12/18/2023]
Abstract
Various protein functions are related to vibrational energy transfer (VET) as an important mechanism. The underlying transfer pathways can be experimentally followed by ultrafast Vis-pump/IR-probe spectroscopy with a donor-sensor pair of non-canonical amino acids (ncAAs) incorporated in a protein. However, so far only one donor ncAA, azulenylalanine (AzAla), exists, which suffers from a comparably low Vis extinction coefficient. Here, we introduce two novel donor ncAAs based on an iminothioindoxyl (ITI) chromophore. The dimethylamino-ITI (DMA-ITI) and julolidine-ITI (J-ITI) moieties overcome the limitation of AzAla with a 50 times higher Vis extinction coefficient. While ITI moieties are known for ultrafast photoswitching, DMA-ITI and J-ITI exclusively form a hot ground state on the sub-ps timescale instead, which is essential for their usage as vibrational energy donor. In VET measurements of donor-sensor dipeptides we investigate the performance of the new donors. We observe 20 times larger signals compared to the established AzAla donor, which opens unprecedented possibilities for the study of VET in proteins.
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Affiliation(s)
- Carolin Feid
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
| | - Larita Luma
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Tobias Fischer
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Jan Gerrit Löffler
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
| | - Nikolai Grebenovsky
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
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4
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Antonio JJ, Kraka E. Noncovalent π Interactions in Mutated Aquomet-Myoglobin Proteins: A QM/MM and Local Vibrational Mode Study. Biochemistry 2023; 62:2325-2337. [PMID: 37458402 DOI: 10.1021/acs.biochem.3c00192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Protein dynamics and function is strongly connected to the energy flow taking place. Myoglobin (Mb) and its mutations are ideal systems to study the process of vibrational energy transfer (VET) at the molecular level. Anti-Stokes ultraviolet resonance Raman studies using a tryptophan (Trp) probe, introduced at different Mb positions by amino acid replacement, have suggested that the amount of VET depends on the position of the Trp probe relative to the heme group. Inspired by this experimental work, we explored the strength of noncovalent π interactions, as well as covalent interactions for both the axial and distal ligands bound to iron in aquomet-Mb with the local vibrational mode analysis (LMA), originally developed by Konkoli and Cremer. Two sets of noncovalent interactions were investigated: (1) the interaction between the water ligand and Trp rings and (2) the interaction between the Trp and the porphyrin rings of the heme group. We assessed the strength of these noncovalent interactions via a special local mode force constant. Various Trp-modified water-bound ferric Mb proteins in the ground state were studied (6 in total) using gas-phase and QM/MM calculations followed by LMA. Our results disclose that VET is indeed dependent on the position of the Trp probe relative to the heme group but also on the tautomeric nature of distal histidine. They provide new guidelines on how to assess noncovalent π interactions in proteins utilizing LMA and how to use these data to explore VET, and more generally protein dynamics and function.
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Affiliation(s)
- Juliana J Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
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5
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Birczyńska-Zych M, Czepiel J, Łabanowska M, Kucharska M, Kurdziel M, Biesiada G, Garlicki A, Wesełucha-Birczyńska A. Course of Plasmodium infection studied using 2D-COS on human erythrocytes. Malar J 2023; 22:188. [PMID: 37340440 DOI: 10.1186/s12936-023-04611-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 05/26/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND The threat of malaria is still present in the world. Recognizing the type of parasite is important in determining a treatment plan. The golden routine involves microscopic diagnostics of Giemsa-stained thin blood smears, however, alternative methods are also constantly being sought, in order to gain an additional insight into the course of the disease. Spectroscopic methods, e.g., Raman spectroscopy, are becoming increasingly popular, due to the non-destructive nature of these techniques. METHODS The study included patients hospitalized for malaria caused by Plasmodium falciparum or Plasmodium vivax, in the Department of Infectious Diseases at the University Hospital in Krakow, Poland, as well as healthy volunteers. The aim of this study was to assess the possibility of using Raman spectroscopy and 2D correlation (2D-COS) spectroscopy in understanding the structural changes in erythrocytes depending on the type of attacking parasite. EPR spectroscopy and two-trace two-dimensional (2T2D) correlation was also used to examine the specificity of paramagnetic centres found in the infected human blood. RESULTS Two-dimensional (2D) correlation spectroscopy facilitates the identification of the hidden relationship, allowing for the discrimination of Raman spectra obtained during the course of disease in human red blood cells, infected by P. falciparum or P. vivax. Synchronous cross-peaks indicate the processes taking place inside the erythrocyte during the export of the parasite protein towards the cell membrane. In contrast, moieties that generate asynchronous 2D cross-peaks are characteristic of the respective ligand-receptor domains. These changes observed during the course of the infection, have different dynamics for P. falciparum and P. vivax, as indicated by the asynchronous correlation cross-peaks. Two-trace two-dimensional (2T2D) spectroscopy, applied to EPR spectra of blood at the beginning of the infection, showed differences between P. falciparum and P. vivax. CONCLUSIONS A unique feature of 2D-COS is the ability to discriminate the collected Raman and EPR spectra. The changes observed during the course of a malaria infection have different dynamics for P. falciparum and P. vivax, indicated by the reverse sequence of events. For each type of parasite, a specific recycling process for iron was observed in the infected blood.
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Affiliation(s)
- Malwina Birczyńska-Zych
- Department of Infectious and Tropical Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
- Department of Infectious Diseases, The University Hospital in Kraków, Jakubowskiego 2, 30-688, Kraków, Poland
| | - Jacek Czepiel
- Department of Infectious and Tropical Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
- Department of Infectious Diseases, The University Hospital in Kraków, Jakubowskiego 2, 30-688, Kraków, Poland
| | - Maria Łabanowska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Martyna Kucharska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Magdalena Kurdziel
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Grażyna Biesiada
- Department of Infectious and Tropical Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
- Department of Infectious Diseases, The University Hospital in Kraków, Jakubowskiego 2, 30-688, Kraków, Poland
| | - Aleksander Garlicki
- Department of Infectious and Tropical Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
- Department of Infectious Diseases, The University Hospital in Kraków, Jakubowskiego 2, 30-688, Kraków, Poland
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6
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Mizutani Y, Mizuno M. Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale. J Chem Phys 2022; 157:240901. [PMID: 36586981 DOI: 10.1063/5.0116734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Vibrational energy exchange between various degrees of freedom is critical to barrier-crossing processes in proteins. Hemeproteins are well suited for studying vibrational energy exchange in proteins because the heme group is an efficient photothermal converter. The released energy by heme following photoexcitation shows migration in a protein moiety on a picosecond timescale, which is observed using time-resolved ultraviolet resonance Raman spectroscopy. The anti-Stokes ultraviolet resonance Raman intensity of a tryptophan residue is an excellent probe for the vibrational energy in proteins, allowing the mapping of energy flow with the spatial resolution of a single amino acid residue. This Perspective provides an overview of studies on vibrational energy flow in proteins, including future perspectives for both methodologies and applications.
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Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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7
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Poudel H, Leitner DM. Energy Transport in Class B GPCRs: Role of Protein-Water Dynamics and Activation. J Phys Chem B 2022; 126:8362-8373. [PMID: 36256609 DOI: 10.1021/acs.jpcb.2c03960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We compute energy exchange networks (EENs) through glucagon-like peptide-1 receptor (GLP-1R), a class B G-protein-coupled receptor (GPCR), in inactive and two active states, one activated by a peptide ligand and the other by a small molecule agonist, from results of molecular dynamics simulations. The reorganized network upon activation contains contributions from structural as well as from dynamic changes and corresponding entropic contributions to the free energy of activation, which are estimated in terms of the change in rates of energy transfer across non-covalent contacts. The role of water in the EENs and in activation of GLP-1R is also investigated. The dynamics of water in contact with the central polar network of the transmembrane region is found to be significantly slower for both activated states compared to the inactive state. This result is consistent with the contribution of water molecules to activation of GLP-1R previously suggested and resembles water dynamics in parts of the transmembrane region found in earlier studies of rhodopsin-like GPCRs.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
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8
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Haliloglu T, Hacisuleyman A, Erman B. Prediction of Allosteric Communication Pathways in Proteins. Bioinformatics 2022; 38:3590-3599. [PMID: 35674396 DOI: 10.1093/bioinformatics/btac380] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/12/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Allostery in proteins is an essential phenomenon in biological processes. In this paper, we present a computational model to predict paths of maximum information transfer between active and allosteric sites. In this information theoretic study, we use mutual information as the measure of information transfer, where transition probability of information from one residue to its contacting neighbors is proportional to the magnitude of mutual information between the two residues. Starting from a given residue and using a Hidden Markov Model, we successively determine the neighboring residues that eventually lead to a path of optimum information transfer. The Gaussian approximation of mutual information between residue pairs is adopted. The limits of validity of this approximation are discussed in terms of a nonlinear theory of mutual information and its reduction to the Gaussian form. RESULTS Predictions of the model are tested on six widely studied cases, CheY Bacterial Chemotaxis, B-cell Lymphoma extra-large Bcl-xL, Human proline isomerase cyclophilin A (CypA), Dihydrofolate reductase DHFR, HRas GTPase, and Caspase-1. The communication transmission rendering the propagation of local fluctuations from the active sites throughout the structure in multiple paths correlate well with the known experimental data. Distinct paths originating from the active site may likely represent a multi functionality such as involving more than one allosteric site and/or preexistence of some other functional states. Our model is computationally fast and simple, and can give allosteric communication pathways, which are crucial for the understanding and control of protein functionality. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Turkan Haliloglu
- Polymer Research Center and Chemical Engineering Department, Bogazici University, 34342, Turkey
| | - Aysima Hacisuleyman
- Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), 1015, Switzerland
| | - Burak Erman
- Chemical and Biological Engineering, Koc University, 34450, Turkey
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9
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Yamashita S, Mizuno M, Takemura K, Kitao A, Mizutani Y. Dependence of Vibrational Energy Transfer on Distance in a Four-Helix Bundle Protein: Equidistant Increments with the Periodicity of α Helices. J Phys Chem B 2022; 126:3283-3290. [PMID: 35467860 DOI: 10.1021/acs.jpcb.2c00956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vibrational energy exchanges between various degrees of freedom are critical to barrier-crossing processes in proteins. Heme proteins are highly suitable for studies of the vibrational energy exchanges in proteins. The migration of excess energy released by heme in a protein moiety can be observed using time-resolved anti-Stokes ultraviolet resonance Raman spectroscopy. The anti-Stokes resonance Raman intensity of a tryptophan residue is an excellent probe for the excess energy and the spatial resolution of a single amino acid residue can be achieved. Here, we studied dependence of vibrational energy transfer on the distance in cytochrome b562, which is a heme-containing, four-helix bundle protein. The vibrational energy transfer from the heme group to a single tryptophan residue introduced by site-directed mutagenesis was examined for different heme-tryptophan distances by a quasi-constant length with the periodicity of α helices. Taken together with structural data obtained by molecular dynamics simulations, the energy transfer could be well described by the model of classical thermal diffusion, which suggests that continuum media provide a good approximation of the protein interior, of which the atomic packing density is very high.
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Affiliation(s)
- Satoshi Yamashita
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kazuhiro Takemura
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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10
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Yamato T, Wang T, Sugiura W, Laprévote O, Katagiri T. Computational Study on the Thermal Conductivity of a Protein. J Phys Chem B 2022; 126:3029-3036. [PMID: 35416670 DOI: 10.1021/acs.jpcb.2c00958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein molecules are thermally fluctuating and tightly packed amino acid residues strongly interact with each other. Such interactions are characterized in terms of heat current at the atomic level. We calculated the thermal conductivity of a small globular protein, villin headpiece subdomain, based on the linear response theory using equilibrium molecular dynamics simulation. The value of its thermal conductivity was 0.3 ± 0.01 [W m-1 K-1], which is in good agreement with experimental and computational studies on the other proteins in the literature. Heat current along the main chain was dominated by local vibrations in the polypeptide bonds, with amide I, II, III, and A bands on the Fourier transform of the heat current autocorrelation function.
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Affiliation(s)
- Takahisa Yamato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tingting Wang
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Wataru Sugiura
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Olivier Laprévote
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takahiro Katagiri
- Information Technology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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11
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Yamashita S, Mizuno M, Mizutani Y. High suitability of tryptophan residues as a spectroscopic thermometer for local temperature in proteins under nonequilibrium conditions. J Chem Phys 2022; 156:075101. [DOI: 10.1063/5.0079797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Satoshi Yamashita
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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12
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Chalopin Y, Sparfel J. Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins. Front Mol Biosci 2022; 8:736376. [PMID: 35004841 PMCID: PMC8733615 DOI: 10.3389/fmolb.2021.736376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
Proteins are among the most complex molecular structures, which have evolved to develop broad functions, such as energy conversion and transport, information storage and processing, communication, and regulation of chemical reactions. However, the mechanisms by which these dynamical entities coordinate themselves to perform biological tasks remain hotly debated. Here, a physical theory is presented to explain how functional dynamical behavior possibly emerge in complex/macro molecules, thanks to the effect that we term bilocalization of thermal vibrations. More specifically, our approach allows us to understand how structural irregularities lead to a partitioning of the energy of the vibrations into two distinct sets of molecular domains, corresponding to slow and fast motions. This shape-encoded spectral allocation, associated to the genetic sequence, provides a close access to a wide reservoir of dynamical patterns, and eventually allows the emergence of biological functions by natural selection. To illustrate our approach, the SPIKE protein structure of SARS-COV2 is considered.
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Affiliation(s)
- Yann Chalopin
- Laboratoire EM2C-CNRS and CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Julien Sparfel
- Laboratoire EM2C-CNRS and CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France
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13
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Poudel H, Leitner DM. Activation-Induced Reorganization of Energy Transport Networks in the β 2 Adrenergic Receptor. J Phys Chem B 2021; 125:6522-6531. [PMID: 34106712 DOI: 10.1021/acs.jpcb.1c03412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We compute energy exchange networks (EENs) through the β2 adrenergic receptor (β2AR), a G-protein coupled receptor (GPCR), in inactive and active states, based on the results of molecular dynamics simulations of this membrane bound protein. We introduce a new definition for the reorganization of EENs upon activation that depends on the relative change in rates of energy transfer across noncovalent contacts throughout the protein. On the basis of the reorganized network that we obtain for β2AR upon activation, we identify a branched pathway between the agonist binding site and the cytoplasmic region, where a G-protein binds to the receptor when activated. The pathway includes all of the motifs containing molecular switches previously identified as contributing to the allosteric transition of β2AR upon agonist binding. EENs and their reorganization upon activation are compared with structure-based contact networks computed for the inactive and active states of β2AR.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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14
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Through bonds or contacts? Mapping protein vibrational energy transfer using non-canonical amino acids. Nat Commun 2021; 12:3284. [PMID: 34078890 PMCID: PMC8172543 DOI: 10.1038/s41467-021-23591-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/06/2021] [Indexed: 11/08/2022] Open
Abstract
Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. Accompanying extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis unravel the VET pathways. Our joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.
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15
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Kumar V, Holtum T, Sebena D, Giese M, Voskuhl J, Schlücker S. Ultraviolet resonance Raman spectroscopy with a continuously tunable picosecond laser: Application to the supramolecular ligand guanidiniocarbonyl pyrrole (GCP). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 250:119359. [PMID: 33418476 DOI: 10.1016/j.saa.2020.119359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
We present a UVRR spectroscopy setup which is equipped with a picosecond pulsed laser excitation source continuously tunable in the 210-2600 nm wavelength range. This laser source is based on a three-stage optical parametric amplifier (OPA) pumped by a bandwidth-compressed second harmonic output of an amplified Yb:KGW laser. It provides <15 cm-1 linewidth pulses below 270 nm, which is sufficient for resolving Raman lines of samples in condensed phase studies. For demonstrating the capability of this tunable setup for UVRR spectroscopy we present its application to the artificial ligand guanidiniocarbonyl pyrrole (GCP), a carboxylate binder used in peptide and protein recognition. A UVRR excitation study in the range 244-310 nm was performed for identifying the optimum laser excitation wavelength for UVRR spectroscopy of this ligand (λmax = 298 nm) at submillimolar concentrations (400 µM) in aqueous solution. The optimum UVRR spectrum is observed for laser excitation with λexc = 266 nm. Only in the relatively narrow range of λexc = 266-275 nm UVRR spectra with a sufficiently high signal-to-noise ratio and without severe interference from autofluorescence (AF) were detectable. At longer excitation wavelengths the UVRR signal is masked by AF. At shorter excitation wavelengths the UVRR spectrum is sufficiently separated from the AF, but the resonance enhancement is not sufficient. The presented tunable UVRR setup provides the flexibility to also identify optimum conditions for other supramolecular ligands for peptide/protein recognition.
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Affiliation(s)
- Vikas Kumar
- Physical Chemistry, Department of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE) and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany.
| | - Tim Holtum
- Physical Chemistry, Department of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE) and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Daniel Sebena
- Organic Chemistry, Department of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Michael Giese
- Organic Chemistry, Department of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Jens Voskuhl
- Organic Chemistry, Department of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry, Department of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE) and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany.
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16
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Reid KM, Yu X, Leitner DM. Change in vibrational entropy with change in protein volume estimated with mode Grüneisen parameters. J Chem Phys 2021; 154:055102. [DOI: 10.1063/5.0039175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Xin Yu
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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17
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Marzolf DR, McKenzie AM, O’Malley MC, Ponomarenko NS, Swaim CM, Brittain TJ, Simmons NL, Pokkuluri PR, Mulfort KL, Tiede DM, Kokhan O. Mimicking Natural Photosynthesis: Designing Ultrafast Photosensitized Electron Transfer into Multiheme Cytochrome Protein Nanowires. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2143. [PMID: 33126541 PMCID: PMC7693585 DOI: 10.3390/nano10112143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 05/02/2023]
Abstract
Efficient nanomaterials for artificial photosynthesis require fast and robust unidirectional electron transfer (ET) from photosensitizers through charge-separation and accumulation units to redox-active catalytic sites. We explored the ultrafast time-scale limits of photo-induced charge transfer between a Ru(II)tris(bipyridine) derivative photosensitizer and PpcA, a 3-heme c-type cytochrome serving as a nanoscale biological wire. Four covalent attachment sites (K28C, K29C, K52C, and G53C) were engineered in PpcA enabling site-specific covalent labeling with expected donor-acceptor (DA) distances of 4-8 Å. X-ray scattering results demonstrated that mutations and chemical labeling did not disrupt the structure of the proteins. Time-resolved spectroscopy revealed three orders of magnitude difference in charge transfer rates for the systems with otherwise similar DA distances and the same number of covalent bonds separating donors and acceptors. All-atom molecular dynamics simulations provided additional insight into the structure-function requirements for ultrafast charge transfer and the requirement of van der Waals contact between aromatic atoms of photosensitizers and hemes in order to observe sub-nanosecond ET. This work demonstrates opportunities to utilize multi-heme c-cytochromes as frameworks for designing ultrafast light-driven ET into charge-accumulating biohybrid model systems, and ultimately for mimicking the photosynthetic paradigm of efficiently coupling ultrafast, light-driven electron transfer chemistry to multi-step catalysis within small, experimentally versatile photosynthetic biohybrid assemblies.
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Affiliation(s)
- Daniel R. Marzolf
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Aidan M. McKenzie
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Matthew C. O’Malley
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Nina S. Ponomarenko
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA; (N.S.P.); (K.L.M.); (D.M.T.)
| | - Coleman M. Swaim
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Tyler J. Brittain
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Natalie L. Simmons
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA;
| | | | - Karen L. Mulfort
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA; (N.S.P.); (K.L.M.); (D.M.T.)
| | - David M. Tiede
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA; (N.S.P.); (K.L.M.); (D.M.T.)
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
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18
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Poudel H, Reid KM, Yamato T, Leitner DM. Energy Transfer across Nonpolar and Polar Contacts in Proteins: Role of Contact Fluctuations. J Phys Chem B 2020; 124:9852-9861. [PMID: 33107736 DOI: 10.1021/acs.jpcb.0c08091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular dynamics simulations of the villin headpiece subdomain HP36 have been carried out to examine relations between rates of vibrational energy transfer across non-covalently bonded contacts and equilibrium structural fluctuations, with focus on van der Waals contacts. Rates of energy transfer across van der Waals contacts vary inversely with the variance of the contact length, with the same constant of proportionality for all nonpolar contacts of HP36. A similar relation is observed for hydrogen bonds, but the proportionality depends on contact pairs, with hydrogen bonds stabilizing the α-helices all exhibiting the same constant of proportionality, one that is distinct from those computed for other polar contacts. Rates of energy transfer across van der Waals contacts are found to be up to 2 orders of magnitude smaller than rates of energy transfer across polar contacts.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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19
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Leitner DM, Hyeon C, Reid KM. Water-mediated biomolecular dynamics and allostery. J Chem Phys 2020; 152:240901. [DOI: 10.1063/5.0011392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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20
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Mizuno M, Mizutani Y. Role of atomic contacts in vibrational energy transfer in myoglobin. Biophys Rev 2020; 12:511-518. [PMID: 32206983 DOI: 10.1007/s12551-020-00681-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/02/2020] [Indexed: 11/26/2022] Open
Abstract
Heme proteins are ideal systems to investigate vibrational energy flow at the atomic level. Upon photoexcitation, a large amount of excess vibrational energy is selectively deposited on heme due to extremely fast internal conversion. This excess energy is redistributed to the surrounding protein moiety and then to water. Vibrational energy flow in myoglobin (Mb) was examined using picosecond time-resolved anti-Stokes ultraviolet resonance Raman (UVRR) spectroscopy. We used the Trp residue directly contacting the heme group as a selective probe for vibrationally excited populations. Trp residues were placed at different position close to the heme by site-directed mutagenesis. This technique allows us to monitor the excess energy on residue-to-residue basis. Anti-Stokes UVRR measurements for Mb mutants suggest that the dominant channel for energy transfer in Mb is the pathway through atomic contacts between heme and nearby amino acid residues as well as that between the protein and solvent water. It is found that energy flow through proteins is analogous to collisional exchange processes in solutions.
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Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.
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21
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Leitner DM, Yamato T. Recent developments in the computational study of protein structural and vibrational energy dynamics. Biophys Rev 2020; 12:317-322. [PMID: 32124240 DOI: 10.1007/s12551-020-00661-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/23/2020] [Indexed: 12/11/2022] Open
Abstract
Recent developments in the computational study of energy transport in proteins are reviewed, including advances in both methodology and applications. The concept of energy exchange network (EEN) is discussed, and a recent calculation of EENs for the allosteric protein FixL is reviewed, which illustrates how residues and protein regions involved in the allosteric transition can be identified. Recent work has examined relations between EENs and protein dynamics as well as structure. We review some of the computational studies carried out on several proteins that explore connections between energy conductivity across polar contacts in proteins and between proteins and water and equilibrium dynamics of the contacts, and we discuss some of the recent experimental work that addresses this topic.
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Affiliation(s)
- David M Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, NV, 89557, USA.
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
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22
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Yamato T, Leitner DM. Structure, dynamics, and energy flow that govern Heme protein functions: theory and experiments. Session 3SBA at the 57th BSJ Annual Meeting. Biophys Rev 2020; 12:291-292. [PMID: 32002759 DOI: 10.1007/s12551-020-00625-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/14/2020] [Indexed: 10/25/2022] Open
Affiliation(s)
- Takahisa Yamato
- Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
| | - David M Leitner
- Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.,Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, NV, 89557, USA
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23
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Reid KM, Yamato T, Leitner DM. Variation of Energy Transfer Rates across Protein–Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin. J Phys Chem B 2020; 124:1148-1159. [DOI: 10.1021/acs.jpcb.9b11413] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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24
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Leitner DM, Pandey HD, Reid KM. Energy Transport across Interfaces in Biomolecular Systems. J Phys Chem B 2019; 123:9507-9524. [DOI: 10.1021/acs.jpcb.9b07086] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Hari Datt Pandey
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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25
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Gulzar A, Valiño Borau L, Buchenberg S, Wolf S, Stock G. Energy Transport Pathways in Proteins: A Non-equilibrium Molecular Dynamics Simulation Study. J Chem Theory Comput 2019; 15:5750-5757. [PMID: 31433644 DOI: 10.1021/acs.jctc.9b00598] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To facilitate the observation of biomolecular energy transport in real time and with single-residue resolution, recent experiments by Baumann et al. ( Angew. Chem. Int. Ed. 2019 , 58 , 2899 , DOI: 10.1002/anie.201812995 ) have used unnatural amino acids β-(1-azulenyl)alanine (Azu) and azidohomoalanine (Aha) to site-specifically inject and probe vibrational energy in proteins. To aid the interpretation of such experiments, non-equilibrium molecular dynamics simulations of the anisotropic energy flow in proteins TrpZip2 and PDZ3 domains are presented. On this account, an efficient simulation protocol is established that accurately mimics the excitation and probing steps of Azu and Aha. The simulations quantitatively reproduce the experimentally found cooling times of the solvated proteins at room temperature and predict that the cooling slows by a factor 2 below the glass temperature of water. In PDZ3, vibrational energy is shown to travel from the initially excited peptide ligand via a complex network of inter-residue contacts and backbone transport to distal regions of the protein. The supposed connection of these energy transport pathways with pathways of allosteric communication is discussed.
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Affiliation(s)
- Adnan Gulzar
- Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany
| | - Luis Valiño Borau
- Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany
| | - Sebastian Buchenberg
- Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany
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26
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Baumann T, Hauf M, Schildhauer F, Eberl KB, Durkin PM, Deniz E, Löffler JG, Acevedo‐Rocha CG, Jaric J, Martins BM, Dobbek H, Bredenbeck J, Budisa N. Ortsaufgelöste Beobachtung von Schwingungsenergietransfer durch ein genetisch codiertes ultraschnelles Heizelement. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812995] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Tobias Baumann
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Matthias Hauf
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Fabian Schildhauer
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Katharina B. Eberl
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | - Patrick M. Durkin
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Erhan Deniz
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | - Jan G. Löffler
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | | | - Jelena Jaric
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
- Derzeitige Adresse: Hospira Zagreb d.o.o.a Pfizer company Prudnicka cesta 60 10291 Prigorje Brdovecko Kroatien
| | - Berta M. Martins
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Unter den Linden 6 10099 Berlin Deutschland
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Unter den Linden 6 10099 Berlin Deutschland
| | - Jens Bredenbeck
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | - Nediljko Budisa
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
- Department of ChemistryUniversity of Manitoba 44 Dysart Rd R3T 2N2 Winnipeg MB Kanada
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27
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Baumann T, Hauf M, Schildhauer F, Eberl KB, Durkin PM, Deniz E, Löffler JG, Acevedo-Rocha CG, Jaric J, Martins BM, Dobbek H, Bredenbeck J, Budisa N. Site-Resolved Observation of Vibrational Energy Transfer Using a Genetically Encoded Ultrafast Heater. Angew Chem Int Ed Engl 2019; 58:2899-2903. [PMID: 30589180 DOI: 10.1002/anie.201812995] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Indexed: 12/22/2022]
Abstract
Allosteric information transfer in proteins has been linked to distinct vibrational energy transfer (VET) pathways in a number of theoretical studies. Experimental evidence for such pathways, however, is sparse because site-selective injection of vibrational energy into a protein, that is, localized heating, is required for their investigation. Here, we solved this problem by the site-specific incorporation of the non-canonical amino acid β-(1-azulenyl)-l-alanine (AzAla) through genetic code expansion. As an exception to Kasha's rule, AzAla undergoes ultrafast internal conversion and heating after S1 excitation while upon S2 excitation, it serves as a fluorescent label. We equipped PDZ3, a protein interaction domain of postsynaptic density protein 95, with this ultrafast heater at two distinct positions. We indeed observed VET from the incorporation sites in the protein to a bound peptide ligand on the picosecond timescale by ultrafast IR spectroscopy. This approach based on genetically encoded AzAla paves the way for detailed studies of VET and its role in a wide range of proteins.
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Affiliation(s)
- Tobias Baumann
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Matthias Hauf
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Fabian Schildhauer
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Katharina B Eberl
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | - Patrick M Durkin
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Erhan Deniz
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | - Jan G Löffler
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | | | - Jelena Jaric
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany.,Present address: Hospira Zagreb d.o.o., a Pfizer company, Prudnicka cesta 60, 10291, Prigorje Brdovecko, Croatia
| | - Berta M Martins
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany.,Department of Chemistry, University of Manitoba, 44 Dysart Rd, R3T 2N2, Winnipeg, MB, Canada
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28
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Ota K, Yamato T. Energy Exchange Network Model Demonstrates Protein Allosteric Transition: An Application to an Oxygen Sensor Protein. J Phys Chem B 2019; 123:768-775. [DOI: 10.1021/acs.jpcb.8b10489] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kunitaka Ota
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takahisa Yamato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, 1 rue Laurent Fries Parc d’Innovation, 67404 Illkirch, Cedex, France
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29
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Abstract
Hemoglobin (Hgb) forms tetramers (dimerized α-β dimers), which enhance its globular stability and may also facilitate small gas molecule transport, as shown by recent all-atom Newtonian solvated simulations. Hydropathic bioinformatic thermodynamic scaling enables close comparisons of hemoglobin dimers with myoglobin and neuroglobin, and reveals many nonlocal wave-like features of strained Hgb structures at the coarse-grained amino acid level. The thermodynamic analysis employs two hydropathic scales, one describing abrupt first-order unfolding transitions, the other continuous second-order transitions. Small molecule exchange at hemes is a first-order process. Wave-like collective tetrameric features appropriate to ligand absorption and release, seen in optical experiments (short times), are identified thermodynamically at long times. Strain fields localized near hemes interfere with extended strain fields associated with dimer interfacial misfit, resulting in novel wavelength dependent dimer correlation function Fano antiresonances.
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Affiliation(s)
- J C Phillips
- Department of Physics and Astronomy , Rutgers University , Piscataway , New Jersey 08854 , United States
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30
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Reid KM, Yamato T, Leitner DM. Scaling of Rates of Vibrational Energy Transfer in Proteins with Equilibrium Dynamics and Entropy. J Phys Chem B 2018; 122:9331-9339. [DOI: 10.1021/acs.jpcb.8b07552] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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