Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems

Short hydrogen bonds, with heavy-atom distances less than 2.7 Å, are believed to exhibit proton delocalization and their possible role in catalysis has been widely debated. While spectroscopic and/or structural methods are usually employed to study the degree of proton delocalization, ambiguities still arise and no direct information on the corresponding potential energy surface is obtained. Here we apply an external electric field to perturb the short hydrogen bond(s) within a collection of green fluorescent protein S65T/H148D variants and photoactive yellow protein mutants, where the chromophore participates in the short hydrogen bond(s) and serves as an optical probe of the proton position. As the proton is charged, its position may shift in response to the external electric field, and the chromophore’s electronic absorption can thus reflect the ease of proton transfer. The results suggest that low-barrier hydrogen bonds are not present within these proteins even when proton affinities between donor and acceptor are closely matched. Exploiting the chromophores as pre-calibrated electrostatic probes, the covalency of short hydrogen bonds as a non-electrostatic component was also revealed. No clear evidence was found for a possible contribution of unusually large polarizabilities of short hydrogen bonds due to proton delocalization; a theoretical framework for this interesting phenomenon is developed.

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Unusual Spectroscopic and Electric Field Sensitivity of a Chromophore with Short Hydrogen Bond: GFP and PYP as Model Systems

10.26434/chemrxiv.12847913 ◽

2020 ◽

Author(s):

Chi-Yun Lin ◽

Steven Boxer

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Electric Field ◽

External Electric Field ◽

Heavy Atom ◽

Model Systems ◽

Donor And Acceptor ◽

Short Hydrogen Bond ◽

Structural Methods ◽

Short Hydrogen Bonds

Short hydrogen bonds, with heavy-atom distances less than 2.7 Å, are believed to exhibit proton delocalization and their possible role in catalysis has been widely debated. While spectroscopic and/or structural methods are usually employed to study the degree of proton delocalization, ambiguities still arise and no direct information on the corresponding potential energy surface is obtained. Here we apply an external electric field to perturb the short hydrogen bond(s) within a collection of green fluorescent protein S65T/H148D variants and photoactive yellow protein mutants, where the chromophore participates in the short hydrogen bond(s) and serves as an optical probe of the proton position. As the proton is charged, its position may shift in response to the external electric field, and the chromophore’s electronic absorption can thus reflect the ease of proton transfer. The results suggest that low-barrier hydrogen bonds are not present within these proteins even when proton affinities between donor and acceptor are closely matched. Exploiting the chromophores as pre-calibrated electrostatic probes, the covalency of short hydrogen bonds as a non-electrostatic component was also revealed. No clear evidence was found for a possible contribution of unusually large polarizabilities of short hydrogen bonds due to proton delocalization; a theoretical framework for this interesting phenomenon is developed.

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Energetics of short hydrogen bonds in photoactive yellow protein

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1113599108 ◽

2011 ◽

Vol 109 (1) ◽

pp. 167-172 ◽

Cited By ~ 41

Author(s):

K. Saito ◽

H. Ishikita

Keyword(s):

Hydrogen Bonds ◽

Photoactive Yellow Protein ◽

Short Hydrogen Bonds

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The proton potential in short hydrogen bonds

Journal of Molecular Structure ◽

10.1016/0022-2860(83)90103-5 ◽

1983 ◽

Vol 100 ◽

pp. 393-402 ◽

Cited By ~ 6

Author(s):

D. Hadži

Keyword(s):

Hydrogen Bonds ◽

Proton Potential ◽

Short Hydrogen Bonds

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Structure of ammonium hydrogen succinate above and below the phase transition around 170K

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768195012432 ◽

1996 ◽

Vol 52 (2) ◽

pp. 323-327 ◽

Cited By ~ 2

Author(s):

A. Hirano ◽

Y. Kubozono ◽

H. Maeda ◽

H. Ishida ◽

S. Kashino

Keyword(s):

Crystal Structure ◽

Phase Transition ◽

Hydrogen Bonds ◽

Order Phase Transition ◽

Space Group ◽

X Ray ◽

Ammonium Hydrogen ◽

Significant Change ◽

Short Hydrogen Bonds ◽

Second Order Phase Transition

For crystals of ammonium hydrogen succinate it is known that the space group is P{\bar 1} with Z = 2 at 293 K and the second-order phase transition occurs around 170 K. X-ray crystal structure analyses above and below 170 K have been carried out in order to study the change in mode of short hydrogen bonds between the hydrogen succinate ions. The space group was determined to be P{\bar 1} at 150 and 190 K by structure analysis. No ordering of the H-atom positions in the short hydrogen bonds occurs by the phase transition. The hydrogen bonds show a decrease in the O...O distances with a decrease in temperature from 290 to 190 K, but no significant change in the geometries between 190 and 150 K. Disorder of the NH4 + ion is not observed at 297, 190 and 150 K. Significant change through the phase transition is found only in the geometry of one of the N—H...O hydrogen bonds between ammonium and hydrogen succinate ions.

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4E-6 Electric Field Sensitivity of Thin Film Resonators Based on Piezoelectric AlN Thin Films

2006 IEEE Ultrasonics Symposium ◽

10.1109/ultsym.2006.125 ◽

2006 ◽

Cited By ~ 3

Author(s):

J. Enlund ◽

V. Yantchev ◽

I. Katardjiev

Keyword(s):

Thin Film ◽

Thin Films ◽

Electric Field ◽

Field Sensitivity ◽

Thin Film Resonators

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Short hydrogen bonds in the catalytic mechanism of serine proteases

Journal of the Serbian Chemical Society ◽

10.2298/jsc0804393l ◽

2008 ◽

Vol 73 (4) ◽

pp. 393-403 ◽

Cited By ~ 5

Author(s):

Vladimir Leskovac ◽

Svetlana Trivic ◽

Draginja Pericin ◽

Mira Popovic ◽

Julijan Kandrac

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Active Site ◽

Serine Proteases ◽

Active Sites ◽

Catalytic Mechanism ◽

Data Bank ◽

Ground State Structure ◽

Low Barrier Hydrogen Bonds ◽

Short Hydrogen Bonds

The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78-1.28 ? revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 ? long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short "low-barrier" hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the "low-barrier hydrogen bond" hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 ? long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the "low-barrier hydrogen bond" hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes.

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