101
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You M, Liu L, Zhang W. The covalently bound diazo group as an infrared probe for hydrogen bonding environments. Phys Chem Chem Phys 2017; 19:19420-19426. [DOI: 10.1039/c7cp01867c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bandwidth or position of diazo groups can probe the polarizability and HBA, or density of HBD groups.
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Affiliation(s)
- Min You
- Center for Advanced Quantum Studies
- Department of Physics and Applied Optics Beijing Area Major Laboratory
- Beijing Normal University
- Beijing
- China
| | - Liyuan Liu
- Center for Advanced Quantum Studies
- Department of Physics and Applied Optics Beijing Area Major Laboratory
- Beijing Normal University
- Beijing
- China
| | - Wenkai Zhang
- Center for Advanced Quantum Studies
- Department of Physics and Applied Optics Beijing Area Major Laboratory
- Beijing Normal University
- Beijing
- China
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102
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Boda M, Naresh Patwari G. Insights into acid dissociation of HCl and HBr with internal electric fields. Phys Chem Chem Phys 2017; 19:7461-7464. [DOI: 10.1039/c6cp08870h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A critical electric field exerted by the solvent on the ionizable group leads to acid dissociation.
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Affiliation(s)
- Manjusha Boda
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
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103
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DiMaio JTM, Raymond DM, Nilsson BL. Display of functional proteins on supramolecular peptide nanofibrils using a split-protein strategy. Org Biomol Chem 2017. [DOI: 10.1039/c7ob01057e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The display of functional proteins on self-assembled peptide nanofibrils is accomplished by noncovalent attachment using a split-protein strategy.
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104
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Fingerhut BP, Costard R, Elsaesser T. Predominance of short range Coulomb forces in phosphate-water interactions—a theoretical analysis. J Chem Phys 2016. [DOI: 10.1063/1.4962755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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105
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Wu Y, Boxer SG. A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase. J Am Chem Soc 2016; 138:11890-5. [PMID: 27545569 PMCID: PMC5063566 DOI: 10.1021/jacs.6b06843] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The vibrational Stark effect (VSE) has been used to measure the electric field in the active site of ketosteroid isomerase (KSI). These measured fields correlate with ΔG(⧧) in a series of conventional mutants, yielding an estimate for the electrostatic contribution to catalysis (Fried et al. Science 2014, 346, 1510-1513). In this work we test this result with much more conservative variants in which individual Tyr residues in the active site are replaced by 3-chlorotyrosine via amber suppression. The electric fields sensed at the position of the carbonyl bond involved in charge displacement during catalysis were characterized using the VSE, where the field sensitivity has been calibrated by vibrational Stark spectroscopy, solvatochromism, and MD simulations. A linear relationship is observed between the electric field and ΔG(⧧) that interpolates between wild-type and more drastic conventional mutations, reinforcing the evaluation of the electrostatic contribution to catalysis in KSI. A simplified model and calculation are developed to estimate changes in the electric field accompanying changes in the extended hydrogen-bond network in the active site. The results are consistent with a model in which the O-H group of a key active site tyrosine functions by imposing a static electrostatic potential onto the carbonyl bond. The model suggests that the contribution to catalysis from the active site hydrogen bonds is of similar weight to the distal interactions from the rest of the protein. A similar linear correlation was also observed between the proton affinity of KSI's active site and the catalytic rate, suggesting a direct connection between the strength of the H-bond and the electric field it exerts.
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Affiliation(s)
- Yufan Wu
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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106
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Kratochvil HT, Carr JK, Matulef K, Annen AW, Li H, Maj M, Ostmeyer J, Serrano AL, Raghuraman H, Moran SD, Skinner JL, Perozo E, Roux B, Valiyaveetil FI, Zanni MT. Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy. Science 2016; 353:1040-1044. [PMID: 27701114 PMCID: PMC5544905 DOI: 10.1126/science.aag1447] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 08/03/2016] [Indexed: 11/02/2022]
Abstract
Potassium channels are responsible for the selective permeation of K+ ions across cell membranes. K+ ions permeate in single file through the selectivity filter, a narrow pore lined by backbone carbonyls that compose four K+ binding sites. Here, we report on the two-dimensional infrared (2D IR) spectra of a semisynthetic KcsA channel with site-specific heavy (13C18O) isotope labels in the selectivity filter. The ultrafast time resolution of 2D IR spectroscopy provides an instantaneous snapshot of the multi-ion configurations and structural distributions that occur spontaneously in the filter. Two elongated features are resolved, revealing the statistical weighting of two structural conformations. The spectra are reproduced by molecular dynamics simulations of structures with water separating two K+ ions in the binding sites, ruling out configurations with ions occupying adjacent sites.
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Affiliation(s)
- Huong T Kratochvil
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua K Carr
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kimberly Matulef
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Alvin W Annen
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Hui Li
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Michał Maj
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jared Ostmeyer
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Arnaldo L Serrano
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - H Raghuraman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sean D Moran
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - J L Skinner
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA.
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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107
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Schneider SH, Boxer SG. Vibrational Stark Effects of Carbonyl Probes Applied to Reinterpret IR and Raman Data for Enzyme Inhibitors in Terms of Electric Fields at the Active Site. J Phys Chem B 2016; 120:9672-84. [PMID: 27541577 DOI: 10.1021/acs.jpcb.6b08133] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases. These results demonstrate that the vibrational Stark effect provides a general framework for estimating the electrostatic contribution to the catalytic rate and may provide a metric for the design or modification of enzymes. Opportunities and limitations of the approach are also described.
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Affiliation(s)
- Samuel H Schneider
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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108
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Al-Ansari IAZ. Physicochemical Properties of Derivatives of N,N-Dimethylamino-cyclic-chalcones: Experimental and Theoretical Study. ChemistrySelect 2016. [DOI: 10.1002/slct.201600458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ibrahim Ahmed Z. Al-Ansari
- Department of Chemistry & Earth Sciences; College of Arts & Sciences -; Qatar University; P.O. Box: 2713 - Doha-Qatar
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109
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Haldar T, Kashid SM, Deb P, Kesh S, Bagchi S. Pick and Choose the Spectroscopic Method to Calibrate the Local Electric Field inside Proteins. J Phys Chem Lett 2016; 7:2456-2460. [PMID: 27295386 DOI: 10.1021/acs.jpclett.6b00852] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Electrostatic interactions in proteins play a crucial role in determining the structure-function relation in biomolecules. In recent years, fluorescent probes have been extensively employed to interrogate the polarity in biological cavities through dielectric constants or semiempirical polarity scales. A choice of multiple spectroscopic methods, not limited by fluorophores, along with a molecular level description of electrostatics involving solute-solvent interactions, would allow more flexibility to pick and choose the experimental technique to determine the local electrostatics within protein interiors. In this work we report that ultraviolet/visible-absorption, infrared-absorption, or (13)C NMR can be used to calibrate the local electric field in both hydrogen bonded and non-hydrogen bonded protein environments. The local electric field at the binding site of a serum protein has been determined using the absorption wavelength as well as the carbonyl stretching frequency of its natural steroid substrate, testosterone. Excellent agreement is observed in the results obtained from two independent spectroscopic techniques.
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Affiliation(s)
- Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Somnath M Kashid
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Pranab Deb
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Sandeep Kesh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
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110
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Wang X, Zhang JZH, He X. Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase. J Chem Phys 2016; 143:184111. [PMID: 26567650 DOI: 10.1063/1.4935176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. In this study, quantum mechanical calculation of protein's internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.
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Affiliation(s)
- Xianwei Wang
- Center for Optics and Optoelectronics Research, College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
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111
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Pan X, Schwartz SD. Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models. J Phys Chem B 2016; 120:6612-20. [PMID: 27347759 DOI: 10.1021/acs.jpcb.6b05119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate. Recent isotope-edited IR spectroscopy suggests that conformational heterogeneity exists within the Michaelis complex of LDH, and this heterogeneity affects the propensity toward the on-enzyme chemical step for each Michaelis substate. By combining molecular dynamics simulations with Markov and hidden Markov models, we obtained a detailed kinetic network of the substates of the Michaelis complex of LDH. The ensemble-average electric fields exerted onto the vibrational probe were calculated to provide a direct comparison with the vibrational spectroscopy. Structural features of the Michaelis substates were also analyzed on atomistic scales. Our work not only clearly demonstrates the conformational heterogeneity in the Michaelis complex of LDH and its coupling to the reactivities of the substates, but it also suggests a methodology to simultaneously resolve kinetics and structures on atomistic scales, which can be directly compared with the vibrational spectroscopy.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
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112
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Abstract
The specific electric field generated by a protease at its active site is considered as an important source of the catalytic power. Accurate calculation of electric field at the active site of an enzyme has both fundamental and practical importance. Measuring site-specific changes of electric field at internal sites of proteins due to, eg, mutation, has been realized by using molecular probes with CO or CN groups in the context of vibrational Stark effect. However, theoretical prediction of change in electric field inside a protein based on a conventional force field, such as AMBER or OPLS, is often inadequate. For such calculation, quantum chemical approach or quantum-based polarizable or polarized force field is highly preferable. Compared with the result from conventional force field, significant improvement is found in predicting experimentally measured mutation-induced electric field change using quantum-based methods, indicating that quantum effect such as polarization plays an important role in accurate description of electric field inside proteins. In comparison, the best theoretical prediction comes from fully quantum mechanical calculation in which both polarization and inter-residue charge transfer effects are included for accurate prediction of electrostatics in proteins.
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Affiliation(s)
- X Wang
- Center for Optics & Optoelectronics Research, College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang, China; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - X He
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.
| | - J Z H Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China; New York University, New York, NY, United States.
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113
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Kuş N. Theoretical and infrared investigation of 2-acetylpyridine isolated in solid nitrogen and in neat condensed phases. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.02.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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114
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Sen S, Boda M, Venkat Lata S, Naresh Patwari G. Internal electric fields in small water clusters [(H2O)n; n = 2-6]. Phys Chem Chem Phys 2016; 18:16730-7. [PMID: 27270616 DOI: 10.1039/c6cp02803a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electric field experienced by a water molecule within a water cluster depends on its position relative to the rest of the water molecules. The stabilization energies and the red-shifts in the donor O-H stretching vibrations in the water clusters increase with the cluster size concomitant with the increase in the electric field experienced by the donor O-H of a particular water molecule due to the hydrogen bonding network. The red-shifts in O-H stretching frequencies show a spread of about ±100 cm(-1) against the corresponding electric fields. Deviations from linearity were marked in the region of 100-160 MV cm(-1), which can be attributed to the strain in the hydrogen bonding network, especially for structures with DDAA and DDA motifs. The linear Stark effect holds up to 200 MV cm(-1) of internal electric field for the average red-shifts in the O-H stretching frequencies, with a Stark tuning rate of 2.4 cm(-1) (MV cm(-1))(-1), suggesting the validity of the classical model in small water clusters.
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Affiliation(s)
- Saumik Sen
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manjusha Boda
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - S Venkat Lata
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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115
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Haldar T, Bagchi S. Electrostatic Interactions Are Key to C═O n-π* Shifts: An Experimental Proof. J Phys Chem Lett 2016; 7:2270-2275. [PMID: 27249517 DOI: 10.1021/acs.jpclett.6b01052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Carbonyl n-π* transitions are known to undergo blue shift in polar and hydrogen-bonding solvents. Using semiempirical expressions, previous studies hypothesized several factors like change in dipole moment and hydrogen-bond strength upon excitation to cause the blue shift. Theoretically, ground-state electrostatics has been predicted to be the key to the observed shifts, however, an experimental proof has been lacking. Our experimental results demonstrate a consistent linear correlation between IR (ground-state phenomenon) and n-π* frequency shifts (involves both ground and excited electronic-states) of carbonyls in hydrogen-bonded and non-hydrogen-bonded environments. The carbonyl hydrogen-bonding status is experimentally verified from deviation in n-π*/fluorescence correlation. The IR/n-π* correlation validates the key role of electrostatic stabilization of the ground state toward n-π* shifts and demonstrates the electrostatic nature of carbonyl hydrogen bonds. n-π* shifts show linear sensitivity to calculated electrostatic fields on carbonyls. Our results portray the potential for n-π* absorption to estimate local polarity in biomolecules and to probe chemical reactions involving carbonyl activation/stabilization.
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Affiliation(s)
- Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
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116
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Deb P, Haldar T, Kashid SM, Banerjee S, Chakrabarty S, Bagchi S. Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins. J Phys Chem B 2016; 120:4034-46. [DOI: 10.1021/acs.jpcb.6b02732] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pranab Deb
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Tapas Haldar
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Somnath M Kashid
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Subhrashis Banerjee
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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117
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Giammanco CH, Kramer PL, Yamada SA, Nishida J, Tamimi A, Fayer MD. Carbon dioxide in an ionic liquid: Structural and rotational dynamics. J Chem Phys 2016; 144:104506. [DOI: 10.1063/1.4943390] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chiara H. Giammanco
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Patrick L. Kramer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Steven A. Yamada
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Jun Nishida
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Amr Tamimi
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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118
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Tamimi A, Fayer MD. Ionic Liquid Dynamics Measured with 2D IR and IR Pump–Probe Experiments on a Linear Anion and the Influence of Potassium Cations. J Phys Chem B 2016; 120:5842-54. [DOI: 10.1021/acs.jpcb.6b00409] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amr Tamimi
- Department
of Chemistry Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department
of Chemistry Stanford University, Stanford, California 94305, United States
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119
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Qin H, Li F, Wang D, Lin H, Jin J. Organized Molecular Interface-Induced Noncrystallizable Polymer Ultrathin Nanosheets with Ordered Chain Alignment. ACS NANO 2016; 10:948-956. [PMID: 26689222 DOI: 10.1021/acsnano.5b06149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The orientation and state of organization of polymer chains play significant roles in determining the final properties and functions of these materials. Unlike most semicrystalline polymers, which have an inherent driving force toward crystallization, the means to control chain packing in noncrystallizable polymers is still restricted and remains a challenge. We report herein a 2D soft template-directed fabrication for ultrathin polyacrylamide nanosheets with a thickness as low as 3.5 nm and large dimensions (>20 μm). More importantly, the polymer chains in the nanosheets produced are well aligned with a clear interchain spacing. The formation of polymer nanosheets with ordered chain alignment was performed in a special solution containing a periodic sandwich structure of lamellar bilayer membranes and water layers that are hundreds of nanometers thick. It functions as a 2D orientation template to align the monomers in an orderly manner along the in-plane direction of the bimolecular membrane via hydrogen bonding.
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Affiliation(s)
- Haili Qin
- i-Lab, CAS Center for Excellence in Nanoscience, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences , Suzhou, Jiangsu 215123, China
- School of Chemistry and Chemical Engineering, Hefei University of Technology , Hefei, Anhui 230009, China
| | - Fujin Li
- i-Lab, CAS Center for Excellence in Nanoscience, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences , Suzhou, Jiangsu 215123, China
| | - Dong Wang
- i-Lab, CAS Center for Excellence in Nanoscience, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences , Suzhou, Jiangsu 215123, China
| | - Hongzhen Lin
- i-Lab, CAS Center for Excellence in Nanoscience, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences , Suzhou, Jiangsu 215123, China
| | - Jian Jin
- i-Lab, CAS Center for Excellence in Nanoscience, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences , Suzhou, Jiangsu 215123, China
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120
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Błasiak B, Ritchie AW, Webb LJ, Cho M. Vibrational solvatochromism of nitrile infrared probes: beyond the vibrational Stark dipole approach. Phys Chem Chem Phys 2016; 18:18094-111. [DOI: 10.1039/c6cp01578f] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Systematic probing of local environments around biopolymers is important for understanding their functions.
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Affiliation(s)
- Bartosz Błasiak
- Center of Molecular Spectroscopy and Dynamics
- Institute of Basic Science (IBS)
- Seoul 02841
- Republic of Korea
- Department of Chemistry
| | - Andrew W. Ritchie
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin
- USA
| | - Lauren J. Webb
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin
- USA
| | - Minhaeng Cho
- Center of Molecular Spectroscopy and Dynamics
- Institute of Basic Science (IBS)
- Seoul 02841
- Republic of Korea
- Department of Chemistry
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121
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Chuntonov L. 2D-IR spectroscopy of hydrogen-bond-mediated vibrational excitation transfer. Phys Chem Chem Phys 2016; 18:13852-60. [DOI: 10.1039/c6cp01640e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Inter-molecular vibrational energy transfer in the hydrogen-bonded complexes of methyl acetate and 4-cyanophenol is studied by dual-frequency 2D-IR spectroscopy.
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Affiliation(s)
- Lev Chuntonov
- Schulich Faculty of Chemistry and Solid State Institute
- Technion – Israel Institute of Technology
- Haifa 32000
- Israel
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122
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List NH, Olsen JMH, Kongsted J. Excited states in large molecular systems through polarizable embedding. Phys Chem Chem Phys 2016; 18:20234-50. [DOI: 10.1039/c6cp03834d] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the polarizable embedding model enables rational design of light-sensitive functional biological materials.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
| | | | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
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123
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Oh KI, Fiorin G, Gai F. How Sensitive is the Amide I Vibration of the Polypeptide Backbone to Electric Fields? Chemphyschem 2015; 16:3595-8. [PMID: 26419214 DOI: 10.1002/cphc.201500777] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Indexed: 01/05/2023]
Abstract
Site-selective isotopic labeling of amide carbonyls offers a nonperturbative means to introduce a localized infrared probe into proteins. Although this strategy has been widely used to investigate various biological questions, the dependence of the underlying amide I vibrational frequency on electric fields (or Stark tuning rate) has not been fully determined, which prevents it from being used in a quantitative manner in certain applications. Herein, through the use of experiments and molecular dynamics simulations, the Stark tuning rate of the amide I vibration of an isotopically labeled backbone carbonyl in a transmembrane α-helix is determined to be approximately 1.4 cm(-1) /(MV/cm). This result provides a quantitative basis for using this vibrational model to assess local electric fields in proteins, among other applications. For instance, by using this value, we are able to show that the backbone region of a dipeptide has a surprisingly low dielectric constant.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA, 19104-6323, USA
| | - Giacomo Fiorin
- Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, PA, 19122-1801, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA, 19104-6323, USA.
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124
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Ritchie AW, Webb LJ. Understanding and Manipulating Electrostatic Fields at the Protein-Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations. J Phys Chem B 2015; 119:13945-57. [PMID: 26375183 DOI: 10.1021/acs.jpcb.5b06888] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological function emerges in large part from the interactions of biomacromolecules in the complex and dynamic environment of the living cell. For this reason, macromolecular interactions in biological systems are now a major focus of interest throughout the biochemical and biophysical communities. The affinity and specificity of macromolecular interactions are the result of both structural and electrostatic factors. Significant advances have been made in characterizing structural features of stable protein-protein interfaces through the techniques of modern structural biology, but much less is understood about how electrostatic factors promote and stabilize specific functional macromolecular interactions over all possible choices presented to a given molecule in a crowded environment. In this Feature Article, we describe how vibrational Stark effect (VSE) spectroscopy is being applied to measure electrostatic fields at protein-protein interfaces, focusing on measurements of guanosine triphosphate (GTP)-binding proteins of the Ras superfamily binding with structurally related but functionally distinct downstream effector proteins. In VSE spectroscopy, spectral shifts of a probe oscillator's energy are related directly to that probe's local electrostatic environment. By performing this experiment repeatedly throughout a protein-protein interface, an experimental map of measured electrostatic fields generated at that interface is determined. These data can be used to rationalize selective binding of similarly structured proteins in both in vitro and in vivo environments. Furthermore, these data can be used to compare to computational predictions of electrostatic fields to explore the level of simulation detail that is necessary to accurately predict our experimental findings.
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Affiliation(s)
- Andrew W Ritchie
- Department of Chemistry, Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology, The University of Texas at Austin , 105 East 24th Street STOP A5300, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry, Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology, The University of Texas at Austin , 105 East 24th Street STOP A5300, Austin, Texas 78712, United States
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125
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List NH, Beerepoot MTP, Olsen JMH, Gao B, Ruud K, Jensen HJA, Kongsted J. Molecular quantum mechanical gradients within the polarizable embedding approach--application to the internal vibrational Stark shift of acetophenone. J Chem Phys 2015; 142:034119. [PMID: 25612701 DOI: 10.1063/1.4905909] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn-Sham density functional theory. As the first application of the implementation, we consider the internal vibrational Stark effect of the C=O group of acetophenone in different solvents and derive its vibrational linear Stark tuning rate using harmonic frequencies calculated from analytical gradients and computed local electric fields. Comparisons to PE calculations employing an enlarged quantum region as well as to a non-polarizable embedding scheme show that the inclusion of mutual polarization between acetophenone and water is essential in order to capture the structural modifications and the associated frequency shifts observed in water. For more apolar solvents, a proper description of dispersion and exchange-repulsion becomes increasingly important, and the quality of the optimized structures relies to a larger extent on the quality of the Lennard-Jones parameters.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Maarten T P Beerepoot
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Bin Gao
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
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126
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Fang B, Wang T, Chen X, Jin T, Zhang R, Zhuang W. Modeling Vibrational Spectra of Ester Carbonyl Stretch in Water and DMSO Based on Molecular Dynamics Simulation. J Phys Chem B 2015; 119:12390-6. [PMID: 26335032 DOI: 10.1021/acs.jpcb.5b06541] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of molecular dynamics simulation, we model the ester carbonyl stretch FTIR signals of methyl acetate in D2O and DMSO. An ab initio map is constructed at the B3LYP/6-311++G** level to relate the carbonyl stretch frequency to the external electric field. Using this map, fluctuating Hamiltonian of the carbonyl stretch is constructed from the MD simulation trajectory. The IR spectra calculated based on this Hamiltonian are found to be in good agreement with the experiment. For methyl acetate in D2O, hydrogen bonding on alkoxy oxygen causes a blue shift of frequency, while that on carbonyl oxygen causes a red shift. Two peaks observed in FTIR signals originate from the balance of these two effects. Furthermore, in both D2O and DMSO solutions, correlations are found between the instantaneous electric field on C═O and the frequencies. Broader line width of the signal in D2O suggests a more inhomogeneous electric field distribution due to the complicated hydrogen-bonding environment.
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Affiliation(s)
- Bin Fang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Tianjun Wang
- Department of Chemistry, ShanghaiTech University , 19 Yueyang Road, Shanghai 200031, China
| | - Xian Chen
- Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), Department of Physics, Jilin University , 2699 Qianjin Street, ChangChun 130012, China
| | - Tan Jin
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Ruiting Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
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127
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Hu F, Wei L, Zheng C, Shen Y, Min W. Live-cell vibrational imaging of choline metabolites by stimulated Raman scattering coupled with isotope-based metabolic labeling. Analyst 2015; 139:2312-7. [PMID: 24555181 DOI: 10.1039/c3an02281a] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Choline is a small molecule that occupies a key position in the biochemistry of all living organisms. Recent studies have strongly implicated choline metabolites in cancer, atherosclerosis and nervous system development. To detect choline and its metabolites, existing physical methods such as magnetic resonance spectroscopy and positron emission tomography are often limited by the poor spatial resolution and substantial radiation dose. Fluorescence imaging, although with submicrometer resolution, requires introduction of bulky fluorophores and thus is difficult in labeling the small choline molecule. By combining the emerging bond-selective stimulated Raman scattering microscopy with metabolic incorporation of deuterated choline, herein we have achieved high resolution imaging of choline-containing metabolites in living mammalian cell lines, primary hippocampal neurons and the multicellular organism C. elegans. Different subcellular distributions of choline metabolites are observed between cancer cells and non-cancer cells, which may reveal a functional difference in the choline metabolism and lipid-mediated signaling events. In neurons, choline incorporation is visualized within both soma and neurites, where choline metabolites are more evenly distributed compared to proteins. Furthermore, choline localization is also observed in the pharynx region of C. elegans larvae, consistent with its organogenesis mechanism. These applications demonstrate the potential of isotope-based stimulated Raman scattering microscopy for future choline-related disease detection and development monitoring in vivo.
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Affiliation(s)
- Fanghao Hu
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY, USA.
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128
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Kramer PL, Nishida J, Giammanco CH, Tamimi A, Fayer MD. Observation and theory of reorientation-induced spectral diffusion in polarization-selective 2D IR spectroscopy. J Chem Phys 2015; 142:184505. [DOI: 10.1063/1.4920949] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Patrick L. Kramer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Jun Nishida
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Chiara H. Giammanco
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Amr Tamimi
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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129
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Fried SD, Boxer SG. Measuring electric fields and noncovalent interactions using the vibrational stark effect. Acc Chem Res 2015; 48:998-1006. [PMID: 25799082 DOI: 10.1021/ar500464j] [Citation(s) in RCA: 318] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Over the past decade, we have developed a spectroscopic approach to measure electric fields inside matter with high spatial (<1 Å) and field (<1 MV/cm) resolution. The approach hinges on exploiting a physical phenomenon known as the vibrational Stark effect (VSE), which ultimately provides a direct mapping between observed vibrational frequencies and electric fields. Therefore, the frequency of a vibrational probe encodes information about the local electric field in the vicinity around the probe. The VSE method has enabled us to understand in great detail the underlying physical nature of several important biomolecular phenomena, such as drug-receptor selectivity in tyrosine kinases, catalysis by the enzyme ketosteroid isomerase, and unidirectional electron transfer in the photosynthetic reaction center. Beyond these specific examples, the VSE has provided a conceptual foundation for how to model intermolecular (noncovalent) interactions in a quantitative, consistent, and general manner. The starting point for research in this area is to choose (or design) a vibrational probe to interrogate the particular system of interest. Vibrational probes are sometimes intrinsic to the system in question, but we have also devised ways to build them into the system (extrinsic probes), often with minimal perturbation. With modern instruments, vibrational frequencies can increasingly be recorded with very high spatial, temporal, and frequency resolution, affording electric field maps correspondingly resolved in space, time, and field magnitude. In this Account, we set out to explain the VSE in broad strokes to make its relevance accessible to chemists of all specialties. Our intention is not to provide an encyclopedic review of published work but rather to motivate the underlying framework of the methodology and to describe how we make and interpret the measurements. Using certain vibrational probes, benchmarked against computer models, it is possible to use the VSE to measure absolute electric fields in arbitrary environments. The VSE approach provides an organizing framework for thinking generally about intermolecular interactions in a quantitative way and may serve as a useful conceptual tool for molecular design.
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Affiliation(s)
- Stephen D. Fried
- Department
of Chemistry; Stanford University, Stanford, California 94305-5080, United States
| | - Steven G. Boxer
- Department
of Chemistry; Stanford University, Stanford, California 94305-5080, United States
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130
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Saggu M, Liu J, Patel A. Identification of Subvisible Particles in Biopharmaceutical Formulations Using Raman Spectroscopy Provides Insight into Polysorbate 20 Degradation Pathway. Pharm Res 2015; 32:2877-88. [PMID: 25773722 PMCID: PMC4526581 DOI: 10.1007/s11095-015-1670-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/05/2015] [Indexed: 11/26/2022]
Abstract
Purpose To study composition and heterogeneity of insoluble subvisible particles in Mab formulations resulting from degradation of polysorbate 20 and to develop a better understanding of the mechanisms of polysorbate degradation leading to particle formation. Methods In this study, we exploit the potential of Raman microscopy for chemical identification of particles in monoclonal antibody formulations. Through a combination of experiments and density functional theory (DFT) calculations, we identified unique spectral marker bands for insoluble degradation products of polysorbate 20. We first applied our methodology to identify particles in model systems containing complex mixtures of fatty acids and then to subvisible particles in antibody formulations stored at 5°C for several years. Results Most of the subvisible particles identified were comprised of mixtures of fatty acids with no observable signal from fatty acid esters consistent with hydrolysis being the predominant degradation mechanism leading to particulate formation under these storage conditions. Conclusions Our methodology is generally applicable for identification of particles in antibody formulations and, in particular, has the potential to give detailed information about particle heterogeneity and insight into mechanistic aspects of particle formation. Electronic supplementary material The online version of this article (doi:10.1007/s11095-015-1670-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miguel Saggu
- Late Stage Pharmaceutical Development, Genentech Inc., South San Francisco, California 94080 USA
| | - Jun Liu
- Late Stage Pharmaceutical Development, Genentech Inc., South San Francisco, California 94080 USA
| | - Ankit Patel
- Late Stage Pharmaceutical Development, Genentech Inc., South San Francisco, California 94080 USA
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131
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Esrafili MD, Mohammadian-Sabet F. Exploring σ-hole bonding in XH3Si···HMY (X=H, F, CN; M=Be, Mg; Y=H, F, CH3) complexes: a “tetrel-hydride” interaction. J Mol Model 2015; 21:60. [DOI: 10.1007/s00894-015-2614-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 02/08/2015] [Indexed: 10/23/2022]
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132
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Affiliation(s)
- Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, 10623 Berlin, Germany.
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133
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Fried SD, Bagchi S, Boxer SG. Extreme electric fields power catalysis in the active site of ketosteroid isomerase. Science 2015; 346:1510-4. [PMID: 25525245 DOI: 10.1126/science.1259802] [Citation(s) in RCA: 323] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Enzymes use protein architecture to impose specific electrostatic fields onto their bound substrates, but the magnitude and catalytic effect of these electric fields have proven difficult to quantify with standard experimental approaches. Using vibrational Stark effect spectroscopy, we found that the active site of the enzyme ketosteroid isomerase (KSI) exerts an extremely large electric field onto the C=O chemical bond that undergoes a charge rearrangement in KSI's rate-determining step. Moreover, we found that the magnitude of the electric field exerted by the active site strongly correlates with the enzyme's catalytic rate enhancement, enabling us to quantify the fraction of the catalytic effect that is electrostatic in origin. The measurements described here may help explain the role of electrostatics in many other enzymes and biomolecular systems.
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Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305-1052, USA
| | - Sayan Bagchi
- Department of Chemistry, Stanford University, Stanford, CA 94305-1052, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-1052, USA.
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134
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Abstract
Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.
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135
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Caplins BW, Lomont JP, Nguyen SC, Harris CB. Vibrational Cooling Dynamics of a [FeFe]-Hydrogenase Mimic Probed by Time-Resolved Infrared Spectroscopy. J Phys Chem A 2014; 118:11529-40. [DOI: 10.1021/jp510517z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Benjamin W. Caplins
- Department
of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Justin P. Lomont
- Department
of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Son C. Nguyen
- Department
of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Charles B. Harris
- Department
of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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136
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Kashid SM, Bagchi S. Experimental Determination of the Electrostatic Nature of Carbonyl Hydrogen-Bonding Interactions Using IR-NMR Correlations. J Phys Chem Lett 2014; 5:3211-3215. [PMID: 26276334 DOI: 10.1021/jz501613p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hydrogen-bonding plays a fundamental role in the structure, function, and dynamics of various chemical and biological systems. Understanding the physical nature of interactions and the role of electrostatics in hydrogen-bonding has been the focus of several theoretical and computational research. We present an experimental approach involving IR-(13)C NMR correlations to determine the electrostatic nature of carbonyl hydrogen-bonding interactions. This report provides a direct experimental evidence of the classical nature of hydrogen-bonding interaction in carbonyls, independent of any theoretical approximation. These results have important implications in chemistry and biology and can be applied to probe the reaction mechanisms involving carbonyl activation/stabilization by hydrogen bonds using spectroscopic techniques.
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Affiliation(s)
- Somnath M Kashid
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Sayan Bagchi
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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137
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Pazos IM, Ghosh A, Tucker MJ, Gai F. Ester carbonyl vibration as a sensitive probe of protein local electric field. Angew Chem Int Ed Engl 2014; 53:6080-4. [PMID: 24788907 PMCID: PMC4104746 DOI: 10.1002/anie.201402011] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 03/20/2014] [Indexed: 11/10/2022]
Abstract
The ability to quantify the local electrostatic environment of proteins and protein/peptide assemblies is key to gaining a microscopic understanding of many biological interactions and processes. Herein, we show that the ester carbonyl stretching vibration of two non-natural amino acids, L-aspartic acid 4-methyl ester and L-glutamic acid 5-methyl ester, is a convenient and sensitive probe in this regard, since its frequency correlates linearly with the local electrostatic field for both hydrogen-bonding and non-hydrogen-bonding environments. We expect that the resultant frequency-electric-field map will find use in various applications. Furthermore, we show that, when situated in a non-hydrogen-bonding environment, this probe can also be used to measure the local dielectric constant (ε). For example, its application to amyloid fibrils formed by Aβ(16-22) revealed that the interior of such β-sheet assemblies has an ε value of approximately 5.6.
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Affiliation(s)
- Ileana M. Pazos
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street, Philadelphia, PA 19104, United States
| | - Ayanjeet Ghosh
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street, Philadelphia, PA 19104, United States
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street, Philadelphia, PA 19104, United States
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138
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Pauszek RF, Kodali G, Stanley RJ. Excited state electronic structures of 5,10-methenyltetrahydrofolate and 5,10-methylenetetrahydrofolate determined by Stark spectroscopy. J Phys Chem A 2014; 118:8320-8. [PMID: 24814224 DOI: 10.1021/jp501143u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Folates are ubiquitous cofactors that participate in a wide variety of critical biological processes. 5,10-Methenyltetrahydrofolate and its photodegradation product 5,10-methylenetetrahydrofolate are both associated with the light-driven DNA repair protein DNA photolyase and its homologues (e.g., cryptochromes). The excited state electronic properties of these folate molecules have been studied here using Stark spectroscopy and complementary quantum calculations. The tetrahydrofolates have relatively large difference dipole moments (ca. 6-8 Debye) and difference polarizabilities (ca. 100 Å(3)). This extensive excited state charge redistribution appears to be due largely to the pendant p-aminobenzoic acid group, which helps shuttle charge over the entirety of the molecule. Simple calculations based on the experimental difference dipole moments suggest that tetrahydrofolates should have large two photon cross sections sufficient to enable two photon microscopy to selectively detect and follow folate-containing proteins both in vitro and in vivo.
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Affiliation(s)
- Raymond F Pauszek
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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139
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Wang X, Li Y, He X, Chen S, Zhang JZH. Effect of strong electric field on the conformational integrity of insulin. J Phys Chem A 2014; 118:8942-52. [PMID: 24796962 DOI: 10.1021/jp501051r] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A series of molecular dynamics (MD) simulations up to 1 μs for bovine insulin monomer in different external electric fields were carried out to study the effect of external electric field on conformational integrity of insulin. Our results show that the secondary structure of insulin is kept intact under the external electric field strength below 0.15 V/nm, but disruption of secondary structure is observed at 0.25 V/nm or higher electric field strength. Although the starting time of secondary structure disruption of insulin is not clearly correlated with the strength of the external electric field ranging between 0.15 and 0.60 V/nm, long time MD simulations demonstrate that the cumulative effect of exposure time under the electric field is a major cause for the damage of insulin's secondary structure. In addition, the strength of the external electric field has a significant impact on the lifetime of hydrogen bonds when it is higher than 0.60 V/nm. The fast evolution of some hydrogen bonds of bovine insulin in the presence of the 1.0 V/nm electric field shows that different microwaves could either speed up protein folding or destroy the secondary structure of globular proteins deponding on the intensity of the external electric field.
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Affiliation(s)
- Xianwei Wang
- State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China
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140
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Pazos IM, Ghosh A, Tucker MJ, Gai F. Ester Carbonyl Vibration as a Sensitive Probe of Protein Local Electric Field. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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141
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Mu X, Wang Q, Wang LP, Fried SD, Piquemal JP, Dalby KN, Ren P. Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. J Phys Chem B 2014; 118:6456-65. [PMID: 24484473 PMCID: PMC4065202 DOI: 10.1021/jp411671a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The charge distribution of halogen
atoms on organochlorine compounds
can be highly anisotropic and even display a so-called σ-hole,
which leads to strong halogen bonds with electron donors. In this
paper, we have systematically investigated a series of chloromethanes
with one to four chloro substituents using a polarizable multipole-based
molecular mechanics model. The atomic multipoles accurately reproduced
the ab initio electrostatic potential around chloromethanes, including
CCl4, which has a prominent σ-hole on the Cl atom.
The van der Waals parameters for Cl were fitted to the experimental
density and heat of vaporization. The calculated hydration free energy,
solvent reaction fields, and interaction energies of several homo-
and heterodimer of chloromethanes are in good agreement with experimental
and ab initio data. This study suggests that sophisticated electrostatic
models, such as polarizable atomic multipoles, are needed for accurate
description of electrostatics in organochlorine compounds and halogen
bonds, although further improvement is necessary for better transferability.
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Affiliation(s)
- Xiaojiao Mu
- Department of Biomedical Engineering, ‡Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Texas 78712, United States
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142
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Ritchie AW, Webb LJ. Optimizing Electrostatic Field Calculations with the Adaptive Poisson–Boltzmann Solver to Predict Electric Fields at Protein–Protein Interfaces II: Explicit Near-Probe and Hydrogen-Bonding Water Molecules. J Phys Chem B 2014; 118:7692-702. [DOI: 10.1021/jp4092656] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andrew W. Ritchie
- Department
of Chemistry,
Center for Nano- and Molecular Science and Technology, and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 1
University Station, A5300, Austin, Texas 78712, United States
| | - Lauren J. Webb
- Department
of Chemistry,
Center for Nano- and Molecular Science and Technology, and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 1
University Station, A5300, Austin, Texas 78712, United States
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143
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Levinson NM, Boxer SG. A conserved water-mediated hydrogen bond network defines bosutinib's kinase selectivity. Nat Chem Biol 2014; 10:127-32. [PMID: 24292070 PMCID: PMC3947016 DOI: 10.1038/nchembio.1404] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 10/11/2013] [Indexed: 01/13/2023]
Abstract
Kinase inhibitors are important cancer drugs, but they tend to display limited target specificity, and their target profiles are often challenging to rationalize in terms of molecular mechanism. Here we report that the clinical kinase inhibitor bosutinib recognizes its kinase targets by engaging a pair of conserved structured water molecules in the active site and that many other kinase inhibitors share a similar recognition mechanism. Using the nitrile group of bosutinib as an infrared probe, we show that the gatekeeper residue and one other position in the ATP-binding site control access of the drug to the structured water molecules and that the amino acids found at these positions account for the kinome-wide target spectrum of the drug. Our work highlights the importance of structured water molecules for inhibitor recognition, reveals a new role for the kinase gatekeeper and showcases an effective approach for elucidating the molecular origins of selectivity patterns.
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Affiliation(s)
- Nicholas M. Levinson
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California, United States of America
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144
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Walker DM, Wang R, Webb LJ. Conserved electrostatic fields at the Ras–effector interface measured through vibrational Stark effect spectroscopy explain the difference in tilt angle in the Ras binding domains of Raf and RalGDS. Phys Chem Chem Phys 2014; 16:20047-60. [DOI: 10.1039/c4cp00743c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Vibrational Stark effect (VSE) spectroscopy was used to measure the electrostatic fields present at the interface of the human guanosine triphosphatase (GTPase) Ras docked with the Ras binding domain (RBD) of the protein kinase Raf.
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Affiliation(s)
- David M. Walker
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology
- and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin, USA
| | - Ruifei Wang
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology
- and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin, USA
| | - Lauren J. Webb
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology
- and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin, USA
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145
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van Wilderen LJGW, Kern-Michler D, Müller-Werkmeister HM, Bredenbeck J. Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy. Phys Chem Chem Phys 2014; 16:19643-53. [DOI: 10.1039/c4cp01498g] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational label SCN is used to report on local structural dynamics in a protein revealing spectral diffusion on a picosecond scale. The SCN spectra are compared to the response of methylthiocyanate in solvents with different polarity and hydrogen-bonding capabilities.
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Affiliation(s)
| | - Daniela Kern-Michler
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- Frankfurt am Main, Germany
| | | | - Jens Bredenbeck
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- Frankfurt am Main, Germany
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146
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Fried SD, Wang LP, Boxer SG, Ren P, Pande VS. Calculations of the electric fields in liquid solutions. J Phys Chem B 2013; 117:16236-48. [PMID: 24304155 DOI: 10.1021/jp410720y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electric field created by a condensed-phase environment is a powerful and convenient descriptor for intermolecular interactions. Not only does it provide a unifying language to compare many different types of interactions, but it also possesses clear connections to experimental observables, such as vibrational Stark effects. We calculate here the electric fields experienced by a vibrational chromophore (the carbonyl group of acetophenone) in an array of solvents of diverse polarities using molecular dynamics simulations with the AMOEBA polarizable force field. The mean and variance of the calculated electric fields correlate well with solvent-induced frequency shifts and band broadening, suggesting Stark effects as the underlying mechanism of these key solution-phase spectral effects. Compared to fixed-charge and continuum models, AMOEBA was the only model examined that could describe nonpolar, polar, and hydrogen bonding environments in a consistent fashion. Nevertheless, we found that fixed-charge force fields and continuum models were able to replicate some results of the polarizable simulations accurately, allowing us to clearly identify which properties and situations require explicit polarization and/or atomistic representations to be modeled properly, and to identify for which properties and situations simpler models are sufficient. We also discuss the ramifications of these results for modeling electrostatics in complex environments, such as proteins.
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Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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147
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Levinson NM, Fried SD, Boxer SG. Solvent-induced infrared frequency shifts in aromatic nitriles are quantitatively described by the vibrational Stark effect. J Phys Chem B 2012; 116:10470-6. [PMID: 22448878 PMCID: PMC3404211 DOI: 10.1021/jp301054e] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physical properties of solvents strongly affect the spectra of dissolved solutes, and this phenomenon can be exploited to gain insight into the solvent-solute interaction. The large solvatochromic shifts observed for many dye molecules in polar solvents are due to variations in the solvent reaction field, and these shifts are widely used to estimate the change in the dye's dipole moment upon photoexcitation, which is typically on the order of ∼1-10 D. In contrast, the change in dipole moment for vibrational transitions is approximately 2 orders of magnitude smaller. Nonetheless, vibrational chromophores display significant solvatochromism, and the relative contributions of specific chemical interactions and electrostatic interactions are debated, complicating the interpretation of vibrational frequency shifts in complex systems such as proteins. Here we present a series of substituted benzonitriles that display widely varying degrees of vibrational solvatochromism. In most cases, this variation can be quantitatively described by the experimentally determined Stark tuning rate, coupled with a simple Onsager-like model of solvation, reinforcing the view that vibrational frequency shifts are largely caused by electrostatic interactions. In addition, we discuss specific cases where continuum solvation models fail to predict solvatochromic shifts, revealing the necessity for more advanced theoretical models that capture local aspects of solute-solvent interactions.
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Affiliation(s)
| | - Stephen D. Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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