All Publications

  • Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields. Journal of the American Chemical Society Kirsh, J. M., Weaver, J. B., Boxer, S. G., Kozuch, J. 2024


    Molecular dynamics (MD) simulations are frequently carried out for proteins to investigate the role of electrostatics in their biological function. The choice of force field (FF) can significantly alter the MD results, as the simulated local electrostatic interactions lack benchmarking in the absence of appropriate experimental methods. We recently reported that the transition dipole moment (TDM) of the popular nitrile vibrational probe varies linearly with the environmental electric field, overcoming well-known hydrogen bonding (H-bonding) issues for the nitrile frequency and, thus, enabling the unambiguous measurement of electric fields in proteins (J. Am. Chem. Soc. 2022, 144 (17), 7562-7567). Herein, we utilize this new strategy to enable comparisons of experimental and simulated electric fields in protein environments. Specifically, previously determined TDM electric fields exerted onto nitrile-containing o-cyanophenylalanine residues in photoactive yellow protein are compared with MD electric fields from the fixed-charge AMBER FF and the polarizable AMOEBA FF. We observe that the electric field distributions for H-bonding nitriles are substantially affected by the choice of FF. As such, AMBER underestimates electric fields for nitriles experiencing moderate field strengths; in contrast, AMOEBA robustly recapitulates the TDM electric fields. The FF dependence of the electric fields can be partly explained by the presence of additional negative charge density along the nitrile bond axis in AMOEBA, which is due to the inclusion of higher-order multipole parameters; this, in turn, begets more head-on nitrile H-bonds. We conclude by discussing the implications of the FF dependence for the simulation of nitriles and proteins in general.

    View details for DOI 10.1021/jacs.3c14775

    View details for PubMedID 38415598

  • Structural Characterization of Fluorescent Proteins Using Tunable Femtosecond Stimulated Raman Spectroscopy. International journal of molecular sciences Chen, C., Henderson, J. N., Ruchkin, D. A., Kirsh, J. M., Baranov, M. S., Bogdanov, A. M., Mills, J. H., Boxer, S. G., Fang, C. 2023; 24 (15)


    The versatile functions of fluorescent proteins (FPs) as fluorescence biomarkers depend on their intrinsic chromophores interacting with the protein environment. Besides X-ray crystallography, vibrational spectroscopy represents a highly valuable tool for characterizing the chromophore structure and revealing the roles of chromophore-environment interactions. In this work, we aim to benchmark the ground-state vibrational signatures of a series of FPs with emission colors spanning from green, yellow, orange, to red, as well as the solvated model chromophores for some of these FPs, using wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in conjunction with quantum calculations. We systematically analyzed and discussed four factors underlying the vibrational properties of FP chromophores: sidechain structure, conjugation structure, chromophore conformation, and the protein environment. A prominent bond-stretching mode characteristic of the quinoidal resonance structure is found to be conserved in most FPs and model chromophores investigated, which can be used as a vibrational marker to interpret chromophore-environment interactions and structural effects on the electronic properties of the chromophore. The fundamental insights gained for these light-sensing units (e.g., protein active sites) substantiate the unique and powerful capability of wavelength-tunable FSRS in delineating FP chromophore properties with high sensitivity and resolution in solution and protein matrices. The comprehensive characterization for various FPs across a colorful palette could also serve as a solid foundation for future spectroscopic studies and the rational engineering of FPs with diverse and improved functions.

    View details for DOI 10.3390/ijms241511991

    View details for PubMedID 37569365

  • Protein protic and aprotic interactions systematically mapped via IR spectroscopy and polarizable molecular dynamics. Biophysical journal Kirsh, J. M., Kozuch, J., Weaver, J. B., Boxer, S. G. 2023; 122 (3S1): 309a

    View details for DOI 10.1016/j.bpj.2022.11.1737

    View details for PubMedID 36783549

  • Carbon-deuterium bonds as reporters of electric fields in solvent and protein environments. Biophysical journal Fried, S. D., Kirsh, J. M., Zheng, C., Mao, Y., Markland, T. E., Boxer, S. G. 2023; 122 (3S1): 481a

    View details for DOI 10.1016/j.bpj.2022.11.2574

    View details for PubMedID 36784478

  • Carbon-deuterium bonds as reporters of electric fields in solvent and protein environments Fried, S. E., Kirsh, J. M., Zheng, C., Mao, Y., Markland, T. E., Boxer, S. G. CELL PRESS. 2023: 481A
  • Protein protic and aprotic interactions systematically mapped via IR spectroscopy and polarizable molecular dynamics Kirsh, J. M., Kozuch, J., Weaver, J. B., Boxer, S. G. CELL PRESS. 2023: 309A
  • Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments. Journal of the American Chemical Society Weaver, J. B., Kozuch, J., Kirsh, J. M., Boxer, S. G. 2022


    Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the -C=N bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.

    View details for DOI 10.1021/jacs.2c00675

    View details for PubMedID 35467853

  • Nitrile IR intensities directly measure electric fields in protic and non-protic environments Weaver, J. B., Kozuch, J. A., Kirsh, J. M., Boxer, S. G. CELL PRESS. 2022: 414A