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Čakić Semenčić M, Kovačević M, Barišić L. Recent Advances in the Field of Amino Acid-Conjugated Aminoferrocenes-A Personal Perspective. Int J Mol Sci 2024; 25:4810. [PMID: 38732028 PMCID: PMC11084972 DOI: 10.3390/ijms25094810] [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: 02/21/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
The development of turn-based inhibitors of protein-protein interactions has attracted considerable attention in medicinal chemistry. Our group has synthesized a series of peptides derived from an amino-functionalized ferrocene to investigate their potential to mimic protein turn structures. Detailed DFT and spectroscopic studies (IR, NMR, CD) have shown that, for peptides, the backbone chirality and bulkiness of the amino acid side chains determine the hydrogen-bond pattern, allowing tuning of the size of the preferred hydrogen-bonded ring in turn-folded structures. However, their biological potential is more dependent on their lipophilicity. In addition, our pioneering work on the chiroptical properties of aminoferrocene-containing peptides enables the correlation of their geometry with the sign of the CD signal in the absorption region of the ferrocene chromophore. These studies have opened up the possibility of using aminoferrocene and its derivatives as chirooptical probes for the determination of various chirality elements, such as the central chirality of amino acids and the helicity of peptide sequences.
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Affiliation(s)
| | | | - Lidija Barišić
- Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (M.Č.S.); (M.K.)
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2
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Rutherford SH, Baker MJ, Hunt NT. 2D-IR spectroscopy of proteins in H 2O-A Perspective. J Chem Phys 2023; 158:030901. [PMID: 36681646 DOI: 10.1063/5.0129480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The form of the amide I infrared absorption band provides a sensitive probe of the secondary structure and dynamics of proteins in the solution phase. However, the frequency coincidence of the amide I band with the bending vibrational mode of H2O has necessitated the widespread use of deuterated solvents. Recently, it has been demonstrated that ultrafast 2D-IR spectroscopy allows the detection of the protein amide I band in H2O-based fluids, meaning that IR methods can now be applied to study proteins in physiologically relevant solvents. In this perspective, we describe the basis of the 2D-IR method for observing the protein amide I band in H2O and show how this development has the potential to impact areas ranging from our fundamental appreciation of protein structural dynamics to new applications for 2D-IR spectroscopy in the analytical and biomedical sciences. In addition, we discuss how the spectral response of water, rather than being a hindrance, now provides a basis for new approaches to data pre-processing, standardization of 2D-IR data collection, and signal quantification. Ultimately, we visualize a direction of travel toward the creation of 2D-IR spectral libraries that can be linked to advanced computational methods for use in high-throughput protein screening and disease diagnosis.
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Affiliation(s)
- Samantha H Rutherford
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Matthew J Baker
- School of Medicine, Faculty of Clinical Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, York YO10 5DD, United Kingdom
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3
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [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] [Indexed: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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4
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Ye X, Wu J, Liang J, Sun Y, Ren X, Ouyang X, Wu D, Li Y, Zhang L, Hu J, Zhang Q, Liu J. Locally Fluorinated Electrolyte Medium Layer for High-Performance Anode-Free Li-Metal Batteries. ACS APPLIED MATERIALS & INTERFACES 2022; 14:53788-53797. [PMID: 36441596 DOI: 10.1021/acsami.2c15452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Low cycling Coulombic efficiency (CE) and messy Li dendrite growth problems have greatly hindered the development of anode-free Li-metal batteries (AFLBs). Thus, functional electrolytes for uniform lithium deposition and lithium/electrolyte side reaction suppression are desired. Here, we report a locally fluorinated electrolyte (LFE) medium layer surrounding Cu foils to tailor the chemical compositions of the solid-electrolyte interphase (SEI) in AFLBs for inhibiting the immoderate Li dendrite growth and to suppress the interfacial reaction. This LFE consists of highly concentrated LiTFSI dissolved in a fluoroethylene carbonate and/or succinonitrile plastic mixture. The CE of Cu||LiNi0.8Co0.1Mn0.1O2 (NCM811) AFLB increased to a high level of 99% as envisaged, and the cycling ability was also highly improved. These improvements are facilitated by the formation of a uniform, dense, and LiF-rich SEI. LiF possesses high interfacial energy at the LiF/Li interface, resulting in a more uniform Li deposition process as proved by density functional theory (DFT) calculation results. This work provides a simple yet utility tech for the enhancement of future high-energy-density AFLBs.
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Affiliation(s)
- Xue Ye
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong518060, China
- College of Energy Engineering, Zhejiang University, Hangzhou310058, China
| | - Jing Wu
- Cryo-EM Center, Southern University of Science and Technology, Shenzhen518055, China
| | - Jianneng Liang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong518060, China
| | - Yipeng Sun
- Department of Mechanical and Materials Engineering, University of Western Ontario, 1151 Richmond St, London, OntarioN6A 3K7, Canada
| | - Xiangzhong Ren
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong518060, China
| | - Xiaoping Ouyang
- College of Energy Engineering, Zhejiang University, Hangzhou310058, China
| | - Dazhuan Wu
- College of Energy Engineering, Zhejiang University, Hangzhou310058, China
| | - Yongliang Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong518060, China
| | - Lei Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong518060, China
| | - Jiangtao Hu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong518060, China
| | - Qianling Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong518060, China
| | - Jianhong Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong518060, China
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5
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Dynamic rotation featured translocations of human serum albumin with a conical glass nanopore. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Zhao R, Shirley JC, Lee E, Grofe A, Li H, Baiz CR, Gao J. Origin of thiocyanate spectral shifts in water and organic solvents. J Chem Phys 2022; 156:104106. [PMID: 35291777 PMCID: PMC8923707 DOI: 10.1063/5.0082969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute-solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies.
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Affiliation(s)
- Ruoqi Zhao
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Joseph C Shirley
- Department of Chemistry, University of Texas, Austin, Texas 78712, USA
| | - Euihyun Lee
- Department of Chemistry, University of Texas, Austin, Texas 78712, USA
| | - Adam Grofe
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Hui Li
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Carlos R Baiz
- Department of Chemistry, University of Texas, Austin, Texas 78712, USA
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
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7
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Yang S, Zhang Q, Yang H, Shi H, Dong A, Wang L, Yu S. Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure. Int J Biol Macromol 2022; 206:175-187. [PMID: 35217087 DOI: 10.1016/j.ijbiomac.2022.02.104] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/21/2022]
Abstract
Infrared (IR) spectroscopy is a highly sensitive technique that provides complete information on chemical compositions. The IR spectra of proteins or peptides give rise to nine characteristic IR absorption bands. The amide I bands are the most prominent and sensitive vibrational bands and widely used to predict protein secondary structures. The interference of H2O absorbance is the greatest challenge for IR protein secondary structure prediction. Much effort has been made to reduce/eliminate the interference of H2O, simplify operation steps, and increase prediction accuracy. Progress in sampling and equipment has rendered the Fourier transform infrared (FTIR) technique suitable for determining the protein secondary structure in broader concentration ranges, greatly simplifying the operating steps. This review highlights the recent progress in sample preparation, data analysis, and equipment development of FTIR in A/T mode, with a focus on recent applications of FTIR spectroscopy in the prediction of protein secondary structure. This review also provides a brief introduction of the progress in ATR-FTIR for predicting protein secondary structure and discusses some combined IR methods, such as AFM-based IR spectroscopy, that are used to analyze protein structural dynamics and protein aggregation.
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Affiliation(s)
- Shouning Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | | | - Huayan Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Haimei Shi
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Aichun Dong
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO, USA.
| | - Li Wang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Shaoning Yu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
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8
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Robben KC, Cheatum CM. Least-Squares Fitting of Multidimensional Spectra to Kubo Line-Shape Models. J Phys Chem B 2021; 125:12876-12891. [PMID: 34783568 PMCID: PMC8630800 DOI: 10.1021/acs.jpcb.1c08764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We report a comprehensive
study of the efficacy of least-squares
fitting of multidimensional spectra to generalized Kubo line-shape
models and introduce a novel least-squares fitting metric, termed
the scale invariant gradient norm (SIGN), that enables a highly reliable
and versatile algorithm. The precision of dephasing parameters is
between 8× and 50× better for nonlinear model fitting compared
to that for the centerline-slope (CLS) method, which effectively increases
data acquisition efficiency by 1–2 orders of magnitude. Whereas
the CLS method requires sequential fitting of both the nonlinear and
linear spectra, our model fitting algorithm only requires nonlinear
spectra but accurately predicts the linear spectrum. We show an experimental
example in which the CLS time constants differ by 60% for independent
measurements of the same system, while the Kubo time constants differ
by only 10% for model fitting. This suggests that model fitting is
a far more robust method of measuring spectral diffusion than the
CLS method, which is more susceptible to structured residual signals
that are not removable by pure solvent subtraction. Statistical analysis
of the CLS method reveals a fundamental oversight in accounting for
the propagation of uncertainty by Kubo time constants in the process
of fitting to the linear absorption spectrum. A standalone desktop
app and source code for the least-squares fitting algorithm are freely
available, with example line-shape models and data. We have written
the MATLAB source code in a generic framework where users may supply
custom line-shape models. Using this application, a standard desktop
fits a 12-parameter generalized Kubo model to a 106 data-point
spectrum in a few minutes.
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Affiliation(s)
- Kevin C Robben
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
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9
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Weng W, Weberg AB, Gera R, Tomson NC, Anna JM. Probing Ligand Effects on the Ultrafast Dynamics of Copper Complexes via Midinfrared Pump-Probe and 2DIR Spectroscopies. J Phys Chem B 2021; 125:12228-12241. [PMID: 34723540 DOI: 10.1021/acs.jpcb.1c06370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of ligand structural variation on the ultrafast dynamics of a series of copper coordination complexes were investigated using polarization-dependent mid-IR pump-probe spectroscopy and two-dimensional infrared (2DIR) spectroscopy. The series consists of three copper complexes [(R3P3tren)CuIIN3]BAr4F (1PR3, R3P3tren = tris[2-(phosphiniminato)ethyl]amine, BAr4F = tetrakis(pentafluorophenyl)borate) where the number of methyl and phenyl groups in the PR3 ligand are systematically varied across the series (PR3 = PMe3, PMe2Ph, PMePh2). The asymmetric stretching mode of azide in the 1PR3 series is used as a vibrational probe of the small-molecule binding site. The results of the pump-probe measurements indicate that the vibrational energy of azide dissipates through intramolecular pathways and that the bulkier phenyl groups lead to an increase in the spatial restriction of the diffusive reorientation of bound azide. From 2DIR experiments, we characterize the spectral diffusion of the azide group and find that an increase in the number of phenyl groups maps to a broader inhomogeneous frequency distribution (Δ2). This indicates that an increase in the steric bulk of the secondary coordination sphere acts to create more distinct configurations in the local environment that are accessible to the azide group. This work demonstrates how ligand structural variation affects the ultrafast dynamics of a small molecular group bound to the metal center, which could provide insight into the structure-function relationship of the copper coordination complexes and transition-metal coordination complexes in general.
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Affiliation(s)
- Wei Weng
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alexander B Weberg
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul Gera
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Neil C Tomson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jessica M Anna
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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10
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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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11
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Ramos S, Mammoser CC, Thibodeau KE, Thielges MC. Dynamics underlying hydroxylation selectivity of cytochrome P450cam. Biophys J 2021; 120:912-923. [PMID: 33545101 PMCID: PMC8008267 DOI: 10.1016/j.bpj.2021.01.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/18/2021] [Accepted: 01/27/2021] [Indexed: 10/22/2022] Open
Abstract
Structural heterogeneity and the dynamics of the complexes of enzymes with substrates can determine the selectivity of catalysis; however, fully characterizing how remains challenging as heterogeneity and dynamics can vary at the spatial level of an amino acid residue and involve rapid timescales. We demonstrate the nascent approach of site-specific two-dimensional infrared (IR) spectroscopy to investigate the archetypical cytochrome P450, P450cam, to better delineate the mechanism of the lower regioselectivity of hydroxylation of the substrate norcamphor in comparison to the native substrate camphor. Specific locations are targeted throughout the enzyme by selectively introducing cyano groups that have frequencies in a spectrally isolated region of the protein IR spectrum as local vibrational probes. Linear and two-dimensional IR spectroscopy were applied to measure the heterogeneity and dynamics at each probe and investigate how they differentiate camphor and norcamphor recognition. The IR data indicate that the norcamphor complex does not fully induce a large-scale conformational change to a closed state of the enzyme adopted in the camphor complex. Additionally, a probe directed at the bound substrate experiences rapidly interconverting states in the norcamphor complex that explain the hydroxylation product distribution. Altogether, the study reveals large- and small-scale structural heterogeneity and dynamics that could contribute to selectivity of a cytochrome P450 and illustrates the approach of site-selective IR spectroscopy to elucidate protein dynamics.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry, Indiana University, Bloomington, Indiana
| | | | | | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana.
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12
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Abstract
This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.
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13
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Acharyya A, Mukherjee D, Gai F. Assessing the Effect of Hofmeister Anions on the Hydrogen-Bonding Strength of Water via Nitrile Stretching Frequency Shift. J Phys Chem B 2020; 124:11783-11792. [PMID: 33346656 DOI: 10.1021/acs.jpcb.0c06299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The temperature dependence of the peak frequency (νmax) of the C≡N stretching vibrational spectrum of a hydrogen-bonded C≡N species is known to be a qualitative measure of its hydrogen-bonding strength. Herein, we show that within a two-state framework, this dependence can be analyzed in a more quantitative manner to yield the enthalpy and entropy changes (ΔHHB and ΔSHB) for the corresponding hydrogen-bonding interactions. Using this method, we examine the effect of ten common anions on the strength of the hydrogen-bond(s) formed between water and the C≡N group of an unnatural amino acid, p-cyanophenylalanine (PheCN). We find that based on the ΔHHB values, these anions can be arranged in the following order: HPO42- > OAc- > F- > SO42- ≈ Cl- ≈ (H2O) ≈ ClO4- ≈ NO3- > Br- > SCN- ≈ I-, which differs from the corresponding Hofmeister series. Because PheCN has a relatively small size, the finding that anions having very different charge densities (e.g., SO42- and ClO4-) act similarly suggests that this ranking order is likely the result of specific ion effects. Since proteins contain different backbone and side-chain units, our results highlight the need to assess their individual contributions toward the overall Hofmeister effect in order to achieve a microscopic understanding of how ions affect the physical and chemical properties of such macromolecules. In addition, the analytical method described in the present study is applicable for analyzing the spectral evolution of any vibrational spectra composed of two highly overlapping bands.
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Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Debopreeti Mukherjee
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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14
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Chalyavi F, Schmitz AJ, Fetto NR, Tucker MJ, Brewer SH, Fenlon EE. Extending the vibrational lifetime of azides with heavy atoms. Phys Chem Chem Phys 2020; 22:18007-18013. [PMID: 32749405 DOI: 10.1039/d0cp02814b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of novel vibrational reporters (VRs), aka infrared (IR) probes, to study local environments and dynamic processes in biomolecules and materials continues to be an important area of research. Azides are important VRs because of their small size and large transition dipole strengths, however, their relatively short vibrational lifetimes (<2 ps) have limited their full potential. Herein we report that the vibrational lifetimes of azides can be increased by attaching them to heavy atoms and by using heavy 15N isotopes. Three group 14 atom triphenyl azides (Ph3CN3, Ph3SiN3, Ph3SnN3), and their triple-15N isotopomers, were synthesized in good yields. Tributyltin azide and its heavy isotopomer (Bu3Sn15N3) were also prepared to probe the effect of molecular scaffolding. The extinction coefficients for the natural abundance azides were determined, ranging from 900 to 1500 M-1 cm-1. The vibrational lifetimes of all azides were measured by pump-probe IR spectroscopy and each showed a major component with a short-to-moderate vibrational lifetime and a minor component with a much longer vibrational lifetime. Based on these results, the lifetime, aka the observation window, of an azide reporter can be extended from ∼2 ps to as long as ∼300 ps by a combination of isotopic labeling and heavy atom effect. 2D IR measurements of these compounds further confirmed the ability to observe these azide transitions at much longer timescales showing their utility to capture dynamic processes from tens to hundreds of picoseconds.
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Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew J Schmitz
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA.
| | - Natalie R Fetto
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA.
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA.
| | - Scott H Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA. ,
| | - Edward E Fenlon
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA. ,
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15
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Bukowski GS, Horness RE, Thielges MC. Involvement of Local, Rapid Conformational Dynamics in Binding of Flexible Recognition Motifs. J Phys Chem B 2019; 123:8387-8396. [PMID: 31535866 DOI: 10.1021/acs.jpcb.9b07036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Flexible protein sequences populate ensembles of rapidly interconverting states differentiated by small-scale fluctuations; however, elucidating whether and how the ensembles determine function experimentally is challenged by the combined high spatial and temporal resolution needed to capture the states. We used carbon-deuterium (C-D) bond vibrations incorporated as infrared probes to characterize with residue-specific detail the heterogeneity of states adopted by proline-rich (PR) sequences and assess their involvement in recognition of Src homology 3 domains. The C-D absorption envelopes provided evidence for two or three sub-populations at all proline residues. The changes in the subpopulations induced by binding generally reflected recognition by conformational selection but depended on the residue and the state of the ligand to illuminate distinct mechanisms among the PR ligands. Notably, the spectral data indicate that greater adaptability among the states is associated with reduced recognition specificity and that perturbation to the ensemble populations contributes to differences in binding entropy. Broadly, the study quantifies rapidly interconverting ensembles with residue-specific detail and implicates them in function.
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Affiliation(s)
- Gregory S Bukowski
- Department of Chemistry , Indiana University, Bloomington , Bloomington , Indiana 47405 , United States
| | - Rachel E Horness
- Department of Chemistry , Indiana University, Bloomington , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Department of Chemistry , Indiana University, Bloomington , Bloomington , Indiana 47405 , United States
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