Jhenny F. Galan

Protein Flexibility and Conformational State: A Comparison of Collective Vibrational Modes of Wild-Type and D96N Bacteriorhodopsin

Far infrared (FIR) spectral measurements of wild-type (WT) and D96N mutant bacteriorhodopsin thin films have been carried out using terahertz time domain spectroscopy as a function of hydration, temperature, and conformational state. The results are compared to calculated spectra generated via normal mode analyses using CHARMM. We find that the FIR absorbance is slowly increasing with frequency and without strong narrow features over the range of 2-60 cm(-1) and up to a resolution of 0.17 cm(-1). The broad absorption shifts in frequency with decreasing temperature as expected with a strongly anharmonic potential and in agreement with neutron inelastic scattering results. Decreasing hydration shifts the absorption to higher frequencies, possibly resulting from decreased coupling mediated by the interior water molecules. Ground-state FIR absorbances have nearly identical frequency dependence, with the mutant having less optical density than the WT. In the M state, the FIR absorbance of the WT increases whereas there is no change for D96N. These results represent the first measurement of FIR absorbance change as a function of conformational state.

Terahertz circular dichroism spectroscopy of biomolecules

Biopolymers such as proteins, DNA and RNA fold into large, macromolecular chiral structures. As charged macromolecules, they absorb strongly in the terahertz due to large-scale collective vibrational modes; as chiral objects, this absorption should be coupled with significant circular dichroism. Terahertz circular dichroism (TCD) is potentially important as a biospecific sensor, unobscured by spectral features related to abiological material. We have constructed atomistic simulations and elastic continuum models of TCD. These models estimate the magnitude of the TCD and the relation between TCD spectroscopic signatures (zero crossings) and the structure, charge distribution and mechanical properties of biomaterials. A broad band TCD spectrometer based on a polarizing interferometer is developed to explore TCD in biomolecules in aqueous solution. Preliminary results on TCD in lysozyme in water at several terahertz frequencies is presented.

Intramolecular Hydrogen Bonding in ortho-Substituted Arylamide Oligomers: A Computational and Experimental Study of ortho-Fluoro- and ortho-Chloro-N-methylbenzamides

As a part of our systematic study of foldamer structural elements, we analyze and quantify the conformational behavior of two model compounds based on a frequently used class of aromatic oligoamide building blocks. Combining computational and NMR approaches, we investigate ortho-fluoro- and ortho-chloro-N-methylbenzamide. Our results indicate that the -F substituent in an ortho position can be used to fine-tune the rigidity of the oligomer backbone. It provides a measurably attenuated but still considerably strong hydrogen bond (H-bond) to the peptide group proton when compared to the -OCH3 substituent in the same position. On the other hand, the ortho-Cl substituent does not impose significant restrictions on the flexibility of the backbone. Its effect on the final shape of an oligomer is likely governed by its size rather than by noncovalent intramolecular interactions. Furthermore, the effect of solvent on the conformational preferences of these building blocks has been quantified. The number of intramolecularly H-bonded conformations decreases significantly when going from nonprotic to protic environments. This study will facilitate rational design of novel arylamide foldamers.

Spectral Tuning of Deep Red Cone Pigments

Visual pigments are G-protein-coupled receptors that provide a critical interface between organisms and their external environment. Natural selection has generated vertebrate pigments that absorb light from the far-UV (360 nm) to the deep red (630 nm) while using a single chromophore, in either the A1 (11- cis-retinal) or A2 (11- cis-3,4-dehydroretinal) form. The fact that a single chromophore can be manipulated to have an absorption maximum across such an extended spectral region is remarkable. The mechanisms of wavelength regulation remain to be fully revealed, and one of the least well-understood mechanisms is that associated with the deep red pigments. We investigate theoretically the hypothesis that deep red cone pigments select a 6- s- trans conformation of the retinal chromophore ring geometry. This conformation is in contrast to the 6- s- cis ring geometry observed in rhodopsin and, through model chromophore studies, the vast majority of visual pigments. Nomographic spectral analysis of 294 A1 and A2 cone pigment literature absorption maxima indicates that the selection of a 6- s- trans geometry red shifts M/LWS A1 pigments by approximately 1500 cm (-1) ( approximately 50 nm) and A2 pigments by approximately 2700 cm (-1) ( approximately 100 nm). The homology models of seven cone pigments indicate that the deep red cone pigments select 6- s- trans chromophore conformations primarily via electrostatic steering. Our results reveal that the generation of a 6- s- trans conformation not only achieves a significant red shift but also provides enhanced stability of the chromophore within the deep red cone pigment binding sites.

Conserved Residues in the Extracellular Loops of Short-Wavelength Cone Visual Pigments

The role of the extracellular loop region of a short-wavelength sensitive pigment, Xenopus violet cone opsin, is investigated via computational modeling, mutagenesis, and spectroscopy. The computational models predict a complex H-bonding network that stabilizes and connects the EC2-EC3 loop and the N-terminus. Mutations that are predicted to disrupt the H-bonding network are shown to produce visual pigments that do not stably bind chromophore and exhibit properties of a misfolded protein. The potential role of a disulfide bond between two conserved Cys residues, Cys(105) in TM3 and Cys(182) in EC2, is necessary for proper folding and trafficking in VCOP. Lastly, certain residues in the EC2 loop are predicted to stabilize the formation of two antiparallel β-strands joined by a hairpin turn, which interact with the chromophore via H-bonding or van der Waals interactions. Mutations of conserved residues result in a decrease in the level of chromophore binding. These results demonstrate that the extracellular loops are crucial for the formation of this cone visual pigment. Moreover, there are significant differences in the structure and function of this region in VCOP compared to that in rhodopsin.

Binding interaction of hypocrellin B to myoglobin: a spectroscopic and computational study.

Hypocrellin B (Hyp B), a perylenequinone naturally present in Hypocrella bambusae, is commonly used to treat a variety of diseases. Its versatile role in different biomedical applications necessitates a thorough investigation of its interaction with different biomolecules, particularly enzymes. To address this need, the binding mode of Hyp B to myoglobin (Mb) was studied using UV-visible absorption, emission, and synchronous fluorescence spectroscopies, as well as flexible docking simulations. Analyses of the absorbance and fluorescence data establish that Hyp B quenches tyrosine (Tyr) and tryptophan (Trp) fluorescence via the formation of two unique ground-state complexes on the surface of Mb, with one site being more energetically preferred than the other (the fraction of fluorophores accessible by Hyp B is 0.32). Molecular modeling simulations demonstrate preferential Hyp B binding at the Tyr103 site first, followed by the Trp7 site. In both cases, a ground-state complex is generated through H-bonding interaction between Hyp B and the respective residues, with the Tyr103 complex being more stable than that of the Trp7 complex. Synchronous fluorescence measurements indicate that the microenvironment surrounding Trp7 becomes more hydrophilic upon Hyp B interaction. This is evidenced by a red-shift of the band associated with this residue, while that of Tyr103 remains the same. Electrostatic potential surfaces reveal a more pronounced shift in electron density of Trp7 upon Hyp B binding compared to Tyr103. The binding constant of Hyp B to Mb is 1.21×10(5)M(-1), suggesting a relatively strong interaction between the ligand and enzyme.