Proteins Proton

Schamagl C, Raupp-Kossmann R, Fischer SF (1999) Molecular basis for pH sensitivity and proton transfer in green fluorescent protein protonation and conformational substates from electrostatic calculations. Biophys J 77 1839-1857... 

We carried out some simulations using two hypothetical models consisting of five ligand protons and five protein protons with the configurations shown in Fig. 2a (the symmetric model) and Fig. 2b (the asymmetric model). 

Even if a given set of protein proton signals P2 and P2 protons in Scheme 2) are instantaneously saturated, the saturation will take a finite time to spread to other protein protons PI and PI sets of protons) and the bound ligand protons ( ) through dipolar networks, and through chemical exchange from the bound to the free ligand (L) protons. This is illustrated in Fig. 3, which... 

It may be noted that the STD intensities are changing even at 3 s of saturation, and generally reach a plateau in intensities at times greater than 4 s. The time-dependent intensity changes in the initial regions (< 0.1 s in Fig. 3) are more reflective of the spatial proximity of the ligand protons to the saturated protein proton in the bound state. 

In Fig. 3b, L2 and L4 have substantially different STD values, with L4 showing significantly smaller effect, even though these two protons are equidistant from the P3 proton. This is a simple consequence of the differences in the relaxation rates for these L2 and L4 protons due to differences in their local environments (e.g., in the asymmetric model, the L4-L5 distance is shorter than the L3-L2 distance, and thus L4-L5 protons experience a faster longitudinal relaxation rate than the L4-L5 protons). These observations suggest that caution is needed in quahtative attempts to relate the magnitudes of steady state STDs to spatial proximity of ligand protons to the protein protons. 

The apparent epitope map based on STDs can exhibit rather significant dependence on which particular protein proton(s) is being saturated. For example, saturation of resolved methyl proton resonances from two separate residues may result in STD spectra with different relative and/or absolute intensities. Similarly, saturation of a specific tyrosine ring proton vs. a specific methyl group can result in different STD spectra. 

There are a variety of models for the magnetic field dependence for polymers and variously ordered phases coming largely from the groups of Kimmich and Noack. We focus here on the protein system that provides unique structural and physical characteristics. Recent advances in the speed of current-switched field-cycling instruments have provided a direct measure of the MRD profile of the protein protons as shown in Fig. 18. The relaxation... 

Yoshioka, S., Y. Aso, and S. Kojima, Softening temperature of lyophilized bovine serum albumin and gamma-globulin as measured by spin-spin relaxation time of protein protons. J Pharm Sci, 1997. 86(4) 470-4. 

It appears that most of the protons that do not exchange are not shielded from water by hydrophobic interaction with lipids since the fraction of exchangeable protons in the amide bonds of residual protein after pronase treatment is approximately the same as in intact ghosts. Indeed this result, together with ORD data, suggests that there is no difference in the gross conformations of the enzymatically accessible and inaccessible protein. Proton exchange is probably inhibited because... 

NOESY experiments aimed at identifying dipolar connectivities between bound water molecules and protein protons have been developed over the last decade [44]. Among them, the ePHOGSY experiment [45] has been successfully applied on paramagnetic metalloproteins [46,47]. 

Figure 5.10 COST versus the RMSD (A) to the target pose for PDF/6. The predicted protein proton chemical shifts were set to the values determined using SHIFTX.

Fig. 14 Aliphatic/aromatic region of NOESY spectrum of a mixture of tubulin, EpoA, and bac-catin III with concentrations of 12 pM, 0.6 mM, and 0.6 mM, respectively. The spectrum was acquired on a 900-MHz spectrometer equipped with a cryoprobe with a mixing time of 70 ms. The blue and green peaks are intramolecular transferred NOE peaks of EpoA and baccatin, respectively. The red peaks represent the interligand transferred NOEs mediated by the protein protons. The numbering of the atoms corresponds to that shown in the compound structures for EpoA (E) and baccatin (B). B-m, B-o, and B-p indicate the protons in the meta, ortho, and para positions of the benzene ring of baccatin, respectively. (Reprinted with permission from [75]. Copyright 2005 Wiley-VCH Verlag GmbH Co. KGaA, Weinheim)...

Peluso, A., Di Donato, M., and Saracino, G.A.A.. (2000) An alternative way of thinking about electron transfer in proteins Proton assisted electron transfer between the primary and the secondary quinones in photosynthetic reaction centers, J. Chem. Phys. 113, 3212-3218. 

Is a carboxylic acid or tyrosine sidechain in a protein protonated or not ... 

Fig. 17. Longitudinal H NMR relaxation parameters at 30 MHz for water adsorbed on lysozyme powders derived from the cross-relaxation model after setting the protein relaxation rate equal to 0. Tis the water proton relaxation time and 7", is the time constant characterizing spin transfer between the protein protons and the water protons. From Hilton etal. (1977).

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