1
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Zheng X, Zhu H, Zhao X, Wang J, Li Q, Zhao X. Emerging affinity methods for protein-drug interaction analysis. J Pharm Biomed Anal 2024; 249:116371. [PMID: 39047466 DOI: 10.1016/j.jpba.2024.116371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
The study of protein-drug interaction plays a crucial role in understanding drug mechanisms, identifying new drug targets and biomarkers, and facilitating drug development and disease treatment. In recent years, significant progress has been made in various protein-drug interaction research methods due to the rapid development and in-depth application of mass spectrometry, nuclear magnetic resonance, Raman spectroscopy, and other technologies. The progress has enhanced the sensitivity, precision, accuracy, and applicability of analytical methods, enabling the establishment of drug-protein interaction networks. This review discusses various emerging research methods, such as native mass spectrometry, infrared spectroscopy, nuclear magnetic resonance and spectrum, biosensor technologies employing surface enhanced Raman, electrochemistry, and magneto resistive signals, as well as affinity magnetic levitation and affinity chromatography. The article also delves into the principles, applications, advantages, and limitations of these technologies.
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Affiliation(s)
- Xinxin Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Huiting Zhu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xue Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
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2
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Hunt NT. Using 2D-IR Spectroscopy to Measure the Structure, Dynamics, and Intermolecular Interactions of Proteins in H 2O. Acc Chem Res 2024; 57:685-692. [PMID: 38364823 PMCID: PMC10918835 DOI: 10.1021/acs.accounts.3c00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024]
Abstract
Infrared (IR) spectroscopy probes molecular structure at the level of the chemical bond or functional group. In the case of proteins, the most informative band in the IR spectrum is the amide I band, which arises predominantly from the C═O stretching vibration of the peptide link. The folding of proteins into secondary and tertiary structures leads to vibrational coupling between peptide units, generating specific amide I spectral signatures that provide a fingerprint of the macromolecular conformation. Ultrafast two-dimensional IR (2D-IR) spectroscopy allows the amide I band of a protein to be spread over a second frequency dimension in a way that mirrors 2D-NMR methods. This means that amide I 2D-IR spectroscopy produces a spectral map that is exquisitely sensitive to protein structure and dynamics and so provides detailed insights that cannot be matched by IR absorption spectroscopy. As a result, 2D-IR spectroscopy has emerged as a powerful tool for probing protein structure and dynamics over a broad range of time and length scales in the solution phase at room temperature. However, the protein amide I band coincides with an IR absorption from the bending vibration of water (δHOH), the natural biological solvent. To circumvent this problem, protein IR studies are routinely performed in D2O solutions because H/D substitution shifts the solvent bending mode (δDOD) to a lower frequency, revealing the amide I band. While effective, this method raises fundamental questions regarding the impact of the change in solvent mass on the structural or solvation dynamics of the protein and the removal of the energetic resonance between solvent and solute.In this Account, a series of studies applying 2D-IR to study the spectroscopy and dynamics of proteins in H2O-rich solvents is reviewed. A comparison of IR absorption spectroscopy and 2D-IR spectroscopy of protein-containing fluids is used to demonstrate the basis of the approach before a series of applications is presented. These range from measurements of fundamental protein biophysics to recent applications of machine learning to gain insight into protein-drug binding in complex mixtures. An outlook is presented, considering the potential for 2D-IR measurements to contribute to our understanding of protein behavior under near-physiological conditions, along with an evaluation of the obstacles that still need to be overcome.
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Affiliation(s)
- Neil T. Hunt
- Department of Chemistry and York Biomedical
Research Institute, University of York, Heslington, York, YO10
5DD, U.K.
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3
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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.
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Affiliation(s)
- Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York Heslington York YO10 5DD UK
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4
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Töpfer K, Upadhyay M, Meuwly M. Quantitative molecular simulations. Phys Chem Chem Phys 2022; 24:12767-12786. [PMID: 35593769 PMCID: PMC9158373 DOI: 10.1039/d2cp01211a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/30/2022] [Indexed: 11/21/2022]
Abstract
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular interactions. The present perspective provides an overview of the present status of quantitative atomistic simulations from colleagues' and our own efforts for gas- and solution-phase processes and for the dynamics on surfaces. Particular attention is paid to direct comparison with experiment. An outlook discusses present challenges and future extensions to bring such dynamics simulations even closer to reality.
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Affiliation(s)
- Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Meenu Upadhyay
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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5
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Meuwly M. Atomistic Simulations for Reactions and Vibrational Spectroscopy in the Era of Machine Learning─ Quo Vadis?. J Phys Chem B 2022; 126:2155-2167. [PMID: 35286087 DOI: 10.1021/acs.jpcb.2c00212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas and in the condensed phase. This Perspective delineates the present status of the field from the efforts of others and some of our own work and discusses open questions and future prospects. The combination of physics-based long-range representations using multipolar charge distributions and kernel representations for the bonded interactions is shown to provide realistic models for the exploration of the infrared spectroscopy of molecules in solution. For reactions, empirical models connecting dedicated energy functions for the reactant and product states allow statistically meaningful sampling of conformational space whereas machine-learned energy functions are superior in accuracy. The future combination of physics-based models with machine-learning techniques and integration into all-purpose molecular simulation software provides a unique opportunity to bring such dynamics simulations closer to reality.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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6
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Mukherjee S, Mondal S, Acharya S, Bagchi B. Tug-of-War between Internal and External Frictions and Viscosity Dependence of Rate in Biological Reactions. PHYSICAL REVIEW LETTERS 2022; 128:108101. [PMID: 35333093 DOI: 10.1103/physrevlett.128.108101] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/13/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
The role of water in biological processes is studied in three reactions, namely, the Fe-CO bond rupture in myoglobin, GB1 unfolding, and insulin dimer dissociation. We compute both internal and external components of friction on relevant reaction coordinates. In all of the three cases, the cross-correlation between forces from protein and water is found to be large and negative that serves to reduce the total friction significantly, increase the calculated reaction rate, and weaken solvent viscosity dependence. The computed force spectrum reveals bimodal 1/f noise, suggesting the use of a non-Markovian rate theory.
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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7
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Chaudhary Y, Bhimalapuram P. Insulin aspart dimer dissociation in water. J Chem Phys 2022; 156:105106. [DOI: 10.1063/5.0078738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Yagya Chaudhary
- International Institute of Information Technology Hyderabad, India
| | - Prabhakar Bhimalapuram
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology Hyderabad, India
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8
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Nijhawan AK, Chan AM, Hsu DJ, Chen LX, Kohlstedt KL. Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures. J Phys Chem B 2021; 125:12401-12412. [PMID: 34748336 PMCID: PMC9096987 DOI: 10.1021/acs.jpcb.1c05820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins have been found to inhabit a diverse set of three-dimensional structures. The dynamics that govern protein interconversion between structures happen over a wide range of time scales─picoseconds to seconds. Our understanding of protein functions and dynamics is largely reliant upon our ability to elucidate physically populated structures. From an experimental structural characterization perspective, we are often limited to measuring the ensemble-averaged structure both in the steady-state and time-resolved regimes. Generating kinetic models and understanding protein structure-function relationships require atomistic knowledge of the populated states in the ensemble. In this Perspective, we present ensemble refinement methodologies that integrate time-resolved experimental signals with molecular dynamics models. We first discuss integration of experimental structural restraints to molecular models in disordered protein systems that adhere to the principle of maximum entropy for creating a complete set of ensemble structures. We then propose strategies to find kinetic pathways between the refined structures, using time-resolved inputs to guide molecular dynamics trajectories and the use of inference to generate tailored stimuli to prepare a desired ensemble of protein states.
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Affiliation(s)
- Adam K Nijhawan
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Arnold M Chan
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Darren J Hsu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Lin X Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Kevin L Kohlstedt
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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9
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Mukherjee S, Acharya S, Mondal S, Banerjee P, Bagchi B. Structural Stability of Insulin Oligomers and Protein Association-Dissociation Processes: Free Energy Landscape and Universal Role of Water. J Phys Chem B 2021; 125:11793-11811. [PMID: 34674526 DOI: 10.1021/acs.jpcb.1c05811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Association and dissociation of proteins are important biochemical events. In this Feature Article, we analyze the available studies of these processes for insulin oligomers in aqueous solution. We focus on the solvation of the insulin monomer in water, stability and dissociation of its dimer, and structural integrity of the hexamer. The intricate role of water in solvation of the dimer- and hexamer-forming surfaces, in long-range interactions between the monomers and the stability of the oligomers, is discussed. Ten water molecules inside the central cavity stabilize the structure of the insulin hexamer. We discuss how different order parameters can be used to understand the dissociation of the insulin dimer. The calculation of the rate using a recently computed multidimensional free energy provides considerable insight into the interplay between protein and water dynamics.
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Puja Banerjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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10
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Acharya S, Mondal S, Mukherjee S, Bagchi B. Rate of Insulin Dimer Dissociation: Interplay between Memory Effects and Higher Dimensionality. J Phys Chem B 2021; 125:9678-9691. [PMID: 34406771 DOI: 10.1021/acs.jpcb.1c03779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We calculate the rate of dissociation of an insulin dimer into two monomers in water. The rate of this complex reaction is determined by multiple factors that are elucidated. By employing advanced sampling techniques, we first obtain the reaction free energy surface for the dimer dissociation as a function of two order parameters, namely, the distance between the center-of-mass of two monomers (R) and the number of cross-contacts (Q) among the backbone Cα atoms of two monomers. We then construct an orthogonal 2D reaction energy surface by introducing the reaction coordinate X to denote the minimum energy pathway and a conjugate coordinate Y that spans the orthogonal direction. The free energy landscape is rugged with multiple maxima and minima. We calculate the rate by employing not only the non-Markovian multidimensional rate theory but also several other theoretical approaches. The necessary reaction frequencies and the frictions are calculated from the time correlation function formalism. Our best estimate of the rate is 0.4 μs-1. Our study reveals interesting opposite influences of dimensionality and memory in determining the rate constant of the reaction. We gain interesting insights into the dimer dissociation process by looking directly at the trajectories obtained from molecular dynamics simulation.
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Affiliation(s)
- Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012 Karnataka, India
| | - Sayantan Mondal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012 Karnataka, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012 Karnataka, India
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11
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Tumbic GW, Hossan MY, Thielges MC. Protein Dynamics by Two-Dimensional Infrared Spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:299-321. [PMID: 34314221 PMCID: PMC8713465 DOI: 10.1146/annurev-anchem-091520-091009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.
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Affiliation(s)
- Goran W Tumbic
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Md Yeathad Hossan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
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12
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Mondal S, Mukherjee S, Acharya S, Bagchi B. Unfolding of Dynamical Events in the Early Stage of Insulin Dimer Dissociation. J Phys Chem B 2021; 125:7958-7966. [PMID: 34260242 DOI: 10.1021/acs.jpcb.1c03104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dissociation of an insulin dimer is an important biochemical event that could also serve as a prototype of dissociations in similar biomolecular assemblies. We use a recently developed multidimensional free energy landscape for insulin dimer dissociation to unearth the microscopic and mechanistic aspects of the initial stages of the process that could hold the key to understanding the stability and the rate. The following sequence of events occurs in the initial stages: (i) The backbone hydrogen bonds break partially at the antiparallel β-sheet junction, (ii) the two α-helices (chain B) move away from each other while several residues (chain A) move closer, and (iii) a flow of adjacent water molecules occurs into the junction region. Interestingly, the intermonomeric center-to-center distance does not increase, but the number of native contacts exhibits a sharp decrease. Subsequent steps involve further disengagement of hydrophobic groups. This process is slow because of an entropic bottleneck created by the existence of the large configuration space available in the native state (NS), which is inhabited by low-frequency conformational fluctuations. We carry out a density-of-states analyses in the dimer NS to unearth distinctive features not present in the monomers. These low-frequency modes are also responsible for a large entropic stabilization of the NS. Hydrophobic disengagement in the early stage leads to the formation of a twisted intermediate state which itself is a metastable minimum (IS-1). The subsequent progress leads to another dimeric complex (IS-2), which is on the dissociative pathway and characterized by a further decrease in the native contacts. The dissociation process provides insights into the workings of a biomolecular assembly.
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Affiliation(s)
- Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Road, Bengaluru, Karnataka 560 012, India
| | - Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Road, Bengaluru, Karnataka 560 012, India
| | - Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Road, Bengaluru, Karnataka 560 012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Road, Bengaluru, Karnataka 560 012, India
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13
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Feng CJ, Sinitskiy A, Pande V, Tokmakoff A. Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity. J Phys Chem B 2021; 125:4620-4633. [PMID: 33929849 DOI: 10.1021/acs.jpcb.1c00399] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic molecular dynamics simulations and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer can be experimentally resolved. Our model reveals two significant conformations to the dimer: a dominant native state consistent with other experimental structures of the dimer and a twisted state with a structure that appears to reflect a ∼55° clockwise rotation of the native dimer interface. The twisted state primarily influences the contacts involving the C-terminus of insulin's B chain, shifting the registry of its intermolecular hydrogen bonds and reorganizing its side-chain packing. The MSM kinetics predict that these configurations exchange on a 14 μs time scale, largely passing through two Markov states with a solvated dimer interface. Computational amide I spectroscopy of site-specifically 13C18O labeled amides indicates that the native and twisted conformation can be distinguished through a series of single and dual labels involving the B24F, B25F, and B26Y residues. Additional structural heterogeneity and disorder is observed within the native and twisted states, and amide I spectroscopy can also be used to gain insight into this variation. This study will provide important interpretive tools for IR spectroscopic investigations of insulin structure and transient IR kinetics experiments studying the conformational dynamics of insulin dimer.
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Affiliation(s)
- Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Anton Sinitskiy
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Vijay Pande
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
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14
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Abstract
The spectroscopic response of and structural dynamics around all azido-modified alanine residues (AlaN3) in lysozyme are characterized. It is found that AlaN3 is a positionally sensitive probe for the local dynamics, covering a frequency range of ∼15 cm-1 for the center frequency of the line shape. This is consistent with findings from selective replacements of amino acids in PDZ2, which reported a frequency span of ∼10 cm-1 for replacements of Val, Ala, or Glu by azidohomoalanine. For the frequency fluctuation correlation functions, the long-time decay constants τ2 range from ∼1 to ∼10 ps, which compares with experimentally measured correlation times of 3 ps. Attaching azide to alanine residues can yield dynamics that decays to zero on the few ps time scale (i.e., static component Δ0 ∼ 0 ps-1) or to a remaining, static contribution of ∼0.5 ps-1 (corresponding to 2.5 cm-1), depending on the local environment on the 10 ps time scale. The magnitude of the static component correlates qualitatively with the degree of hydration of the spectroscopic probe. Although attaching azide to alanine residues is found to be structurally minimally invasive with respect to the overall protein structure, analysis of the local hydrophobicity indicates that the hydration around the modification site differs for modified and unmodified alanine residues, respectively.
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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15
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El Khoury Y, Le Breton G, Cunha AV, Jansen TLC, van Wilderen LJGW, Bredenbeck J. Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c. J Chem Phys 2021; 154:124201. [PMID: 33810651 DOI: 10.1063/5.0039969] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.
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Affiliation(s)
- Youssef El Khoury
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Guillaume Le Breton
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ana V Cunha
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Luuk J G W van Wilderen
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
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16
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Hsu DJ, Leshchev D, Kosheleva I, Kohlstedt KL, Chen LX. Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations. J Chem Phys 2021; 154:105101. [PMID: 33722011 PMCID: PMC7943248 DOI: 10.1063/5.0039194] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
The protein folding process often proceeds through partially folded transient states. Therefore, a structural understanding of these disordered states is crucial for developing mechanistic models of the folding process. Characterization of unfolded states remains challenging due to their disordered nature, and incorporating multiple methods is necessary. Combining the time-resolved x-ray solution scattering (TRXSS) signal with molecular dynamics (MD), we are able to characterize transient partially folded states of bovine α-lactalbumin, a model system widely used for investigation of molten globule states, during its unfolding triggered by a temperature jump. We track the unfolding process between 20 µs and 70 ms and demonstrate that it passes through three distinct kinetic states. The scattering signals associated with these transient species are then analyzed with TRXSS constrained MD simulations to produce protein structures that are compatible with the input signals. Without utilizing any experimentally extracted kinetic information, the constrained MD simulation successfully drove the protein to an intermediate molten globule state; signals for two later disordered states are refined to terminal unfolded states. From our examination of the structural characteristics of these disordered states, we discuss the implications disordered states have on the folding process, especially on the folding pathway. Finally, we discuss the potential applications and limitations of this method.
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Affiliation(s)
- Darren J. Hsu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Denis Leshchev
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kevin L. Kohlstedt
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Lin X. Chen
- Authors to whom correspondence should be addressed: and
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17
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Salehi SM, Koner D, Meuwly M. Dynamics and Infrared Spectrocopy of Monomeric and Dimeric Wild Type and Mutant Insulin. J Phys Chem B 2020; 124:11882-11894. [PMID: 33245663 DOI: 10.1021/acs.jpcb.0c08048] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The infrared spectroscopy and dynamics of -CO labels in wild type and mutant insulin monomer and dimer are characterized from molecular dynamics simulations using validated force fields. It is found that the spectroscopy of monomeric and dimeric forms in the region of the amide-I vibration differs for residues B24-B26 and D24-D26, which are involved in dimerization of the hormone. Also, the spectroscopic signatures change for mutations at position B24 from phenylalanine, which is conserved in many organisms and is known to play a central role in insulin aggregation, to alanine or glycine. Using three different methods to determine the frequency trajectories (solving the nuclear Schrödinger equation on an effective 1-dimensional potential energy curve, using instantaneous normal modes, and using parametrized frequency maps) leads to the same overall conclusions. The spectroscopic response of monomeric WT and mutant insulin differs from that of their respective dimers, and the spectroscopy of the two monomers in the dimer is also not identical. For the WT and F24A and F24G monomers, spectroscopic shifts are found to be ∼20 cm-1 for residues (B24-B26) located at the dimerization interface. Although the crystal structure of the dimer is that of a symmetric homodimer, dynamically the two monomers are not equivalent on the nanosecond time scale. Together with earlier work on the thermodynamic stability of the WT and the same mutants, it is concluded that combining computational and experimental infrared spectroscopy provides a potentially powerful way to characterize the aggregation state and dimerization energy of modified insulins.
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Debasish Koner
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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18
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Antoszewski A, Feng CJ, Vani BP, Thiede EH, Hong L, Weare J, Tokmakoff A, Dinner AR. Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding. J Phys Chem B 2020; 124:5571-5587. [PMID: 32515958 PMCID: PMC7774804 DOI: 10.1021/acs.jpcb.0c03521] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The protein hormone insulin exists in various oligomeric forms, and a key step in binding its cellular receptor is dissociation of the dimer. This dissociation process and its corresponding association process have come to serve as paradigms of coupled (un)folding and (un)binding more generally. Despite its fundamental and practical importance, the mechanism of insulin dimer dissociation remains poorly understood. Here, we use molecular dynamics simulations, leveraging recent developments in umbrella sampling, to characterize the energetic and structural features of dissociation in unprecedented detail. We find that the dissociation is inherently multipathway with limiting behaviors corresponding to conformational selection and induced fit, the two prototypical mechanisms of coupled folding and binding. Along one limiting path, the dissociation leads to detachment of the C-terminal segment of the insulin B chain from the protein core, a feature believed to be essential for receptor binding. We simulate IR spectroscopy experiments to aid in interpreting current experiments and identify sites where isotopic labeling can be most effective for distinguishing the contributions of the limiting mechanisms.
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Affiliation(s)
- Adam Antoszewski
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chi-Jui Feng
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bodhi P Vani
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Erik H Thiede
- Department of Computer Science, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Statistics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lu Hong
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jonathan Weare
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Aaron R Dinner
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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19
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Zhang XX, Tokmakoff A. Revealing the Dynamical Role of Co-solvents in the Coupled Folding and Dimerization of Insulin. J Phys Chem Lett 2020; 11:4353-4358. [PMID: 32401513 PMCID: PMC7850624 DOI: 10.1021/acs.jpclett.0c00982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Solvent-protein interactions are important for protein biological functions, especially for a coupled folding and binding system such as insulin. By monitoring the change in the conformation of insulin dimers during dissociation with temperature-jump infrared spectroscopy, we show that co-solvents can significantly destabilize the dimers by perturbing their hydrophobic center. The transition from the native to intermediate dimer state is observed as the buried residues are exposed to solvents in the presence of 10% dimethyl sulfoxide and with α-helices unfolding when ethanol is present, which reduces the dissociation time dramatically to 50% and 20% of the value in a D2O solution, respectively. We propose a self-consistent analysis using complementary methods to resolve this coupled folding and binding process and obtain a much higher rate of monomer association than of intermediate folding. Our results demonstrate that the conformational changes are critical in dimer formation and strongly affected by co-solvents.
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Affiliation(s)
- Xin-Xing Zhang
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
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20
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Gong Q, Zhang H, Zhang H, Chen C. Calculating the absolute binding free energy of the insulin dimer in an explicit solvent. RSC Adv 2020; 10:790-800. [PMID: 35494470 PMCID: PMC9047981 DOI: 10.1039/c9ra08284k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/23/2019] [Indexed: 12/23/2022] Open
Abstract
Insulin is a significant hormone in the regulation of glucose level in the blood. Its monomers bind to each other to form dimers or hexamers through a complex process. To study the binding of the insulin dimer, we first calculate its absolute binding free energy by the steered molecular dynamics method and the confinement method based on a fictitious thermodynamic cycle. After considering some special correction terms, the final calculated binding free energy at 298 K is −8.97 ± 1.41 kcal mol−1, which is close to the experimental value of −7.2 ± 0.8 kcal mol−1. Furthermore, we discuss the important residue–residue interactions between the insulin monomers, including hydrophobic interactions, π–π interactions and hydrogen bond interactions. The analysis reveals five key residues, VlaB12, TyrB16, PheB24, PheB25, and TyrB26, for the dimerization of the insulin. We also perform MM-PBSA calculations for the wild-type dimer and some mutants and study the roles of the key residues by the change of the binding energy of the insulin dimer. In this paper, we calculate the absolute binding free energy of an insulin dimer by steered MD method. The result of −8.97 kcal mol−1 is close to the experimental value −7.2 kcal mol−1. We also analyze the residue–residue interactions.![]()
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Affiliation(s)
- Qiankun Gong
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Haomiao Zhang
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Haozhe Zhang
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
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21
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Flanagan JC, Baiz CR. Ultrafast pH-jump two-dimensional infrared spectroscopy. OPTICS LETTERS 2019; 44:4937-4940. [PMID: 31613233 DOI: 10.1364/ol.44.004937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
We present a pH-jump two-dimensional infrared (2D IR) spectrometer to probe pH-dependent conformational changes from nanoseconds to milliseconds. The design incorporates a nanosecond 355 nm source into a pulse-shaper-based 2D IR spectrometer to trigger dissociation of a caged proton prior to probing subsequent conformational changes with femtosecond 2D IR spectroscopy. We observe a blue shift in the amide I mode (C═O stretch) of diglycine induced by protonation of the terminal amine. This method combines the bond-specific structural sensitivity of ultrafast 2D IR with triggered conformational dynamics, providing structural access to multiscale biomolecular transformations such as protein folding.
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22
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Minnes L, Greetham GM, Shaw DJ, Clark IP, Fritzsch R, Towrie M, Parker AW, Henry AJ, Taylor RJ, Hunt NT. Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy. J Phys Chem B 2019; 123:8733-8739. [PMID: 31557034 PMCID: PMC7007250 DOI: 10.1021/acs.jpcb.9b08870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
The signaling protein
calmodulin (CaM) undergoes a well-known change
in secondary structure upon binding Ca2+, but the structural
plasticity of the Ca2+-free apo state
is linked to CaM functionality. Variable temperature studies of apo-CaM indicate two structural transitions at 46 and 58
°C that are assigned to melting of the C- and N-terminal domains,
respectively, but the molecular mechanism of domain unfolding is unknown.
We report temperature-jump time-resolved infrared (IR) spectroscopy
experiments designed to target the first steps in the C-terminal domain
melting transition of human apo-CaM. A comparison
of the nonequilibrium relaxation of apo-CaM with
the more thermodynamically stable holo-CaM, with
4 equiv of Ca2+ bound, shows that domain melting of apo-CaM begins on microsecond time scales with α-helix
destabilization. These observations enable the assignment of previously
reported dynamics of CaM on hundreds of microsecond time scales to
thermally activated melting, producing a complete mechanism for thermal
unfolding of CaM.
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Affiliation(s)
- Lucy Minnes
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Robby Fritzsch
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | | | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , United Kingdom
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23
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Label-free measurements on the solution of monomeric and dimeric insulin using a periodical terahertz split ring resonator. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Sarkar D, Kang P, Nielsen SO, Qin Z. Non-Arrhenius Reaction-Diffusion Kinetics for Protein Inactivation over a Large Temperature Range. ACS NANO 2019; 13:8669-8679. [PMID: 31268674 PMCID: PMC7384293 DOI: 10.1021/acsnano.9b00068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding protein folding and unfolding has been a long-standing fundamental question and has important applications in manipulating protein activity in biological systems. Experimental investigations of protein unfolding have been predominately conducted by small temperature perturbations (e.g., temperature jump), while molecular simulations are limited to small time scales (microseconds) and high temperatures to observe unfolding. Thus, it remains unclear how fast a protein unfolds irreversibly and loses function (i.e., inactivation) across a large temperature range. In this work, using nanosecond pulsed heating of individual plasmonic nanoparticles to create precise localized heating, we examine the protein inactivation kinetics at extremely high temperatures. Connecting this with protein inactivation measurements at low temperatures, we observe that the kinetics of protein unfolding is less sensitive to temperature change at the higher temperatures, which significantly departs from the Arrhenius behavior extrapolated from low temperatures. To account for this effect, we propose a reaction-diffusion model that modifies the temperature-dependence of protein inactivation by introducing a diffusion limit. Analysis of the reaction-diffusion model provides general guidelines in the behavior of protein inactivation (reaction-limited, transition, diffusion-limited) across a large temperature range from physiological temperature to extremely high temperatures. We further demonstrate that the reaction-diffusion model is particularly useful for designing optimal operating conditions for protein photoinactivation. The experimentally validated reaction-diffusion kinetics of protein unfolding is an important step toward understanding protein-inactivation kinetics over a large temperature range. It has important applications including molecular hyperthermia and calls for future studies to examine this model for other protein molecules.
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Affiliation(s)
- Daipayan Sarkar
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Peiyuan Kang
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Steven O. Nielsen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Zhenpeng Qin
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Surgery, The University of Texas at Southwestern Medical Center, Dallas, TX 75390, USA
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25
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Dong X, Ranganathan S, Qu G, Piazza CL, Belfort M. Structural accommodations accompanying splicing of a group II intron RNP. Nucleic Acids Res 2019; 46:8542-8556. [PMID: 29790987 PMCID: PMC6144810 DOI: 10.1093/nar/gky416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/03/2018] [Indexed: 01/21/2023] Open
Abstract
Group II introns, the putative progenitors of spliceosomal introns and retrotransposons, are ribozymes that are capable of self-splicing and DNA invasion. In the cell, group II introns form ribonucleoprotein (RNP) complexes with an intron-encoded protein, which is essential to folding, splicing and retromobility of the intron. To understand the structural accommodations underlying splicing, in preparation for retromobility, we probed the endogenously expressed Lactococcus lactis Ll.LtrB group II intron RNP using SHAPE. The results, which are consistent in vivo and in vitro, provide insights into the dynamics of the intron RNP as well as RNA-RNA and RNA-protein interactions. By comparing the excised intron RNP with mutant RNPs in the precursor state, confined SHAPE profile differences were observed, indicative of rearrangements at the active site as well as disengagement at the functional RNA-protein interface in transition between the two states. The exon-binding sequences in the intron RNA, which interact with the 5' exon and the target DNA, show increased flexibility after splicing. In contrast, stability of major tertiary and protein interactions maintains the scaffold of the RNA through the splicing transition, while the active site is realigned in preparation for retromobility.
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Affiliation(s)
- Xiaolong Dong
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Srivathsan Ranganathan
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Guosheng Qu
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Carol Lyn Piazza
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
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26
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Wang P, Wang X, Liu L, Zhao H, Qi W, He M. The Hydration Shell of Monomeric and Dimeric Insulin Studied by Terahertz Time-Domain Spectroscopy. Biophys J 2019; 117:533-541. [PMID: 31326108 DOI: 10.1016/j.bpj.2019.06.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 06/04/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022] Open
Abstract
Protein aggregation is believed to be a significant biological mechanism related to neurodegenerative disease, which makes the early-stage detection of aggregates a major concern. We demonstrated the use of terahertz (THz) time-domain spectroscopy to study protein-water interaction of monomeric and dimeric bovine insulin in aqueous samples. Regulated by changing pH and verified by size-exclusion chromatography and dynamic light scattering, we then measured their concentration-dependent changes in THz absorption between 0.5 and 3.0 THz and quantitatively deduced the extended hydration shell thickness by cubic distribution model and random distribution model. Under a random distribution assumption, the extended hydration thickness is 15.4 ± 0.4 Å for monomeric insulin and 17.5 ± 0.5 Å for dimeric insulin, with the hydration number of 6700 and 11,000, respectively. The hydration number of dimeric insulin is not twice but 1.64 times that of monomeric insulin, further supported by the ratio of solvent-accessible surface area. This "1.64-times" relation probably originates from the structural and conformational changes accompanied with dimerization. Combined with the investigations on insulin samples with different single amino acid mutations, residue B24 is believed to play an important role in the dimerization process. It is demonstrated that THz time-domain spectroscopy is a useful tool and has the sensitivity to provide the hydration information of different protein aggregates at an early stage.
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Affiliation(s)
- Pengfei Wang
- State Key Laboratory of Precision Measuring Technology and Instruments
| | | | - Liyuan Liu
- Key Laboratory of Optoelectronic Information Technology, Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China
| | - Hongwei Zhao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering
| | - Mingxia He
- State Key Laboratory of Precision Measuring Technology and Instruments.
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27
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Desmond JL, Koner D, Meuwly M. Probing the Differential Dynamics of the Monomeric and Dimeric Insulin from Amide-I IR Spectroscopy. J Phys Chem B 2019; 123:6588-6598. [PMID: 31318551 DOI: 10.1021/acs.jpcb.9b04628] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The monomer-dimer equilibrium for insulin is one of the essential steps in forming the receptor-binding competent monomeric form of the hormone. Despite this importance, the thermodynamic stability, in particular for modified insulins, is quite poorly understood, in part, due to experimental difficulties. This work explores one- and two-dimensional infrared spectroscopy in the range of the amide-I band for the hydrated monomeric and dimeric wild-type hormone. It is found that for the monomer the frequency fluctuation correlation function (FFCF) and the one-dimensional infrared spectra are position sensitive. The spectra of the -CO probes at the dimerization interface (residues Phe24, Phe25, and Tyr26) split and indicate an asymmetry despite the overall (formal) point symmetry of the dimer structure. Also, the decay times of the FFCF for the same -CO probe in the monomer and the dimer can differ by up to 1 order of magnitude, for example, for residue PheB24, which is solvent exposed for the monomer but at the interface for the dimer. The spectroscopic shifts correlate approximately with the average number of hydration waters and the magnitude of the FFCF at time zero. However, this correlation is only qualitative due to the heterogeneous and highly dynamical environment. Based on density functional theory calculations, the dominant contribution for solvent-exposed -CO is found to arise from the surrounding water (∼75%), whereas the protein environment contributes considerably less. The results suggest that infrared spectroscopy is a positionally sensitive probe of insulin dimerization, in particular in conjunction with isotopic labeling of the probe.
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Affiliation(s)
- Jasmine L Desmond
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , 4056 Basel , Switzerland
| | - Debasish Koner
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , 4056 Basel , Switzerland
| | - Markus Meuwly
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , 4056 Basel , Switzerland
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28
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Zheng X, Yu P, Wang J. Ultrafast intramolecular vibrational energy transfer in carbon nitride hydrocolloid examined by femtosecond two-dimensional infrared spectroscopy. J Chem Phys 2019; 150:194703. [PMID: 31117771 DOI: 10.1063/1.5093542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In this work, ultrafast vibrational and structural processes in a graphitic carbon nitride hydrocolloid system were studied using a combination of linear infrared and nonlinear two-dimensional infrared (2D IR) spectroscopies. The experimentally observed three IR line shapes in the C=N stretching vibration frequency region were analyzed and attributed to the rigid and conjugated molecular frame of the prepared g-CN molecular species, which is believed to be a dimeric tris-s-triazine, as well as attributed to insignificant solvent influence on the delocalized C=N vibrations. Vibrational transition density cubes were also computed for the proposed g-CN dimer, confirming the heterocyclic C=N stretching nature of the three IR absorption peaks. Intramolecular vibrational energy transfer dynamics and spectral diffusion of the g-CN system were characterized by examining a series of time-dependent 2D IR spectra. A picosecond intramolecular vibrational energy redistribution process was found to occur among these delocalized C=N stretching modes, acting as an efficient vibrational energy transfer channel. This work reasonably connects the experimentally observed IR signature to a specific g-CN structure and also provides the first report on the ultrafast intramolecular processes of such carbon nitride systems. The obtained results are fundamentally important for understanding the molecular mechanisms of such carbon-nitride based functional materials.
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Affiliation(s)
- Xuan Zheng
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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29
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Ramos S, Thielges MC. Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition. J Phys Chem B 2019; 123:3551-3566. [PMID: 30848912 DOI: 10.1021/acs.jpcb.9b00969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteins exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires knowledge of the populated states and thus the experimental tools to characterize them. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution, and 2D IR methods that provide richer information are becoming more routine. Although application of IR spectroscopy for investigation of proteins is challenged by spectral congestion, the issue can be overcome by site-specific introduction of amino acid side chains that have IR probe groups with frequency-resolved absorptions, which furthermore enables selective characterization of different locations in proteins. Here, we briefly introduce the biophysical methods and summarize the current progress toward the study of proteins. We then describe our efforts to apply site-specific 1D and 2D IR spectroscopy toward elucidation of protein conformations and dynamics to investigate their involvement in protein molecular recognition, in particular mediated by dynamic complexes: plastocyanin and its binding partner cytochrome f, cytochrome P450s and substrates or redox partners, and Src homology 3 domains and proline-rich peptide motifs. We highlight the advantages of frequency-resolved probes to characterize specific, local sites in proteins and uncover variation among different locations, as well as the advantage of the fast time scale of IR spectroscopy to detect rapidly interconverting states. In addition, we illustrate the greater insight provided by 2D methods and discuss potential routes for further advancement of the field of biomolecular 2D IR spectroscopy.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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30
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Banerjee P, Mondal S, Bagchi B. Effect of ethanol on insulin dimer dissociation. J Chem Phys 2019; 150:084902. [PMID: 30823756 DOI: 10.1063/1.5079501] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Insulin-dimer dissociation is an essential biochemical process required for the activity of the hormone. We investigate this dissociation process at the molecular level in water and at the same time, in 5% and 10% water-ethanol mixtures. We compute the free energy surface of the protein dissociation processes by employing biased molecular dynamics simulation. In the presence of ethanol (EtOH), we observe a marked lowering in the free energy barrier of activation of dimer dissociation from that in the neat water, by as much as ∼50%, even in the 5% water-ethanol solution. In addition, ethanol is found to induce significant changes in the dissociation pathway. We extract the most probable conformations of the intermediate states along the minimum energy pathway in the case of all the three concentrations (EtOH mole fractions 0, 5, and 10). We explore the change in microscopic structures that occur in the presence of ethanol. Interestingly, we discover a stable intermediate state in the water-ethanol binary mixture where the centers of the monomers are separated by about 3 nm and the contact order parameter is close to zero. This intermediate is stabilized by the wetting of the interface between the two monomers by the preferential distribution of ethanol and water molecules. This wetting serves to reduce the free energy barrier significantly and thus results in an increase in the rate of dimer dissociation. We also analyze the solvation of the two monomers during the dissociation and both the proteins' departure from the native state configuration to obtain valuable insights into the dimer dissociation processes.
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Affiliation(s)
- Puja Banerjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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31
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Banerjee P, Mondal S, Bagchi B. Insulin dimer dissociation in aqueous solution: A computational study of free energy landscape and evolving microscopic structure along the reaction pathway. J Chem Phys 2018; 149:114902. [DOI: 10.1063/1.5042290] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Puja Banerjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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32
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Hogle DG, Cunningham AR, Tucker MJ. Equilibrium versus Nonequilibrium Peptide Dynamics: Insights into Transient 2D IR Spectroscopy. J Phys Chem B 2018; 122:8783-8795. [PMID: 30040900 DOI: 10.1021/acs.jpcb.8b05063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the past two decades, two-dimensional infrared (2D IR) spectroscopy has evolved from the theoretical underpinnings of nonlinear spectroscopy as a means of investigating detailed molecular structure on an ultrafast time scale. The combined time and spectral resolution over which spectra can be collected on complex molecular systems has led to the precise structural resolution of dynamic species that have previously been impossible to directly observe through traditional methods. The adoption of 2D IR spectroscopy for the study of protein folding and peptide interactions has provided key details of how small changes in conformations can exert major influences on the activities of these complex molecular systems. Traditional 2D IR experiments are limited to molecules under equilibrium conditions, where small motions and fluctuations of these larger molecules often still lead to functionality. Utilizing techniques that allow the rapid initiation of chemical or structural changes in conjunction with 2D IR spectroscopy, i.e., transient 2D IR, a vast dynamic range becomes available to the spectroscopist uncovering structural content far from equilibrium. Furthermore, this allows the observation of reaction pathways of these macromolecules under quasi- and nonequilibrium conditions.
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Affiliation(s)
- David G Hogle
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Amy R Cunningham
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Matthew J Tucker
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
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Rimmerman D, Leshchev D, Hsu DJ, Hong J, Abraham B, Kosheleva I, Henning R, Chen LX. Insulin hexamer dissociation dynamics revealed by photoinduced T-jumps and time-resolved X-ray solution scattering. Photochem Photobiol Sci 2018; 17:874-882. [PMID: 29855030 DOI: 10.1039/c8pp00034d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structural dynamics of insulin hexamer dissociation were studied by the photoinduced temperature jump technique and monitored by time-resolved X-ray scattering. The process of hexamer dissociation was found to involve several transient intermediates, including an expanded hexamer and an unstable tetramer. Our findings provide insights into the mechanisms of protien-protein association.
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Affiliation(s)
- Dolev Rimmerman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA.
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Rimmerman D, Leshchev D, Hsu DJ, Hong J, Abraham B, Henning R, Kosheleva I, Chen LX. Probing Cytochrome c Folding Transitions upon Phototriggered Environmental Perturbations Using Time-Resolved X-ray Scattering. J Phys Chem B 2018; 122:5218-5224. [PMID: 29709179 DOI: 10.1021/acs.jpcb.8b03354] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Direct tracking of protein structural dynamics during folding-unfolding processes is important for understanding the roles of hierarchic structural factors in the formation of functional proteins. Using cytochrome c (cyt c) as a platform, we investigated its structural dynamics during folding processes triggered by local environmental changes (i.e., pH or heme iron center oxidation/spin/ligation states) with time-resolved X-ray solution scattering measurements. Starting from partially unfolded cyt c, a sudden pH drop initiated by light excitation of a photoacid caused a structural contraction in microseconds, followed by active site restructuring and unfolding in milliseconds. In contrast, the reduction of iron in the heme via photoinduced electron transfer did not affect conformational stability at short timescales (<1 ms), despite active site coordination geometry changes. These results demonstrate how different environmental perturbations can change the nature of interaction between the active site and protein conformation, even within the same metalloprotein, which will subsequently affect the folding structural dynamics.
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Affiliation(s)
- Dolev Rimmerman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Denis Leshchev
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Darren J Hsu
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Jiyun Hong
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Baxter Abraham
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Robert Henning
- Center for Advanced Radiation Sources , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Irina Kosheleva
- Center for Advanced Radiation Sources , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Lin X Chen
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States.,Chemical Sciences and Engineering Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
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35
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Hutson WO, Spencer AP, Harel E. Ultrafast Four-Dimensional Coherent Spectroscopy by Projection Reconstruction. J Phys Chem Lett 2018; 9:1034-1040. [PMID: 29432694 DOI: 10.1021/acs.jpclett.8b00122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Multidimensional coherent spectroscopy provides insights into the vibronic structure and dynamics of complex systems. In general, the higher the dimensionality, the better the spectral discrimination and the more information that may be extracted about the system. A major impediment to widespread implementation of these methods, however, is that the acquisition time generally increases exponentially with dimensionality, prohibiting practical implementation. We demonstrate the use of nonuniform sampling based on the projection-slice theorem and inverse Radon transform within the context of a fifth-order, 4D technique (GAMERS) designed to correlate the vibrational contributions to different electronic states. Projection-reconstruction (PRO GAMERS) greatly reduces the data sampling requirements without sacrificing frequency resolution. The sensitivity of this technique is demonstrated to surpass conventional uniform sampling by orders of magnitude. The incorporation of projection-reconstruction into multidimensional coherent spectroscopy opens up the possibility to study the structure of complex chemical, biological, and physical systems with unprecedented detail.
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Affiliation(s)
- William O Hutson
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Austin P Spencer
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Elad Harel
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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36
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Kraack JP. Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods. Top Curr Chem (Cham) 2017; 375:86. [PMID: 29071445 DOI: 10.1007/s41061-017-0172-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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Minnes L, Shaw DJ, Cossins BP, Donaldson PM, Greetham GM, Towrie M, Parker AW, Baker MJ, Henry AJ, Taylor RJ, Hunt NT. Quantifying Secondary Structure Changes in Calmodulin Using 2D-IR Spectroscopy. Anal Chem 2017; 89:10898-10906. [DOI: 10.1021/acs.analchem.7b02610] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Lucy Minnes
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, United Kingdom
| | | | | | - Paul M. Donaldson
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Michael Towrie
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Matthew J. Baker
- WestCHEM,
Department of Pure and Applied Chemistry, Technology and Innovation
Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, United Kingdom
| | | | | | - Neil T. Hunt
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, United Kingdom
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38
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Rimmerman D, Leshchev D, Hsu DJ, Hong J, Kosheleva I, Chen LX. Direct Observation of Insulin Association Dynamics with Time-Resolved X-ray Scattering. J Phys Chem Lett 2017; 8:4413-4418. [PMID: 28853898 PMCID: PMC5804350 DOI: 10.1021/acs.jpclett.7b01720] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Biological functions frequently require protein-protein interactions that involve secondary and tertiary structural perturbation. Here we study protein-protein dissociation and reassociation dynamics in insulin, a model system for protein oligomerization. Insulin dimer dissociation into monomers was induced by a nanosecond temperature-jump (T-jump) of ∼8 °C in aqueous solution, and the resulting protein and solvent dynamics were tracked by time-resolved X-ray solution scattering (TRXSS) on time scales of 10 ns to 100 ms. The protein scattering signals revealed the formation of five distinguishable transient species during the association process that deviate from simple two-state kinetics. Our results show that the combination of T-jump pump coupled to TRXSS probe allows for direct tracking of structural dynamics in nonphotoactive proteins.
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Affiliation(s)
- Dolev Rimmerman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Denis Leshchev
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Darren J. Hsu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jiyun Hong
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lin X. Chen
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
- Corresponding Author, ,
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