Proteins fluctuation frequency

We have emphasized here that the dynamic aspects of NMR studies are crucially important for structurally or dynamically heterogeneous systems such as synthetic or natural hydrogels, protein fibrils and membrane proteins. This is in order to characterize their unique chemical, physical and biological properties in terms of a variety of fluctuation frequencies, including high (> 108 Hz) or intermediate (104-105 Hz) frequency fluctuations. It turns out that the presence of the high-frequency motions, which are readily evaluated by comparative CPMAS and DDMAS studies, is... 

A from the surfaces by accelerated Mn " -induced spin-relaxation [227]. The fluctuation frequency of the remaining TM core is of the order of 10 Hz based on the chemical shift differences [223]. It is suggested that motions in the 10 ps correlation regime may be functionaUy important for the photocycle of bR, and protein-Upid interactions are motionaUy coupled in this dynamic regime [228]. 

Diacylglycerol kinase (DGK) from E. coli is a small 121 amino-add, integral membrane protein which catalyzes the conversion of diacylglycerol and MgATP to phosphatic acid and MgADP. DGK is homotrimeric and each monomeric component contains three TM hehces. The NMR spectra of [3- C]Ala-, [l- C]Val-DGK are broadened to yield rather featureless peaks at physiological temperatures, both in DM solution or the hquid crystalline lipid bilayers, due to the dynamic interference of fluctuation frequencies of DGK with frequencies of MAS or proton decoupling of lO" or 10 Hz, respectively [261]. 

Nonnal mode analysis was first applied to proteins in the early 1980s [1-3]. Much of the literature on normal mode analysis of biological molecules concerns the prediction of functionally relevant motions. In these studies it is always assumed that the soft normal modes, i.e., those with the lowest frequencies and largest fluctuations, are the ones that are functionally relevant. The ultimate justification for this assumption must come from comparisons to experimental data. Several studies have been made in which the predictions of a normal mode analysis have been compared to functional transitions derived from two X-ray conformers [4-7]. These smdies do indeed suggest that the low frequency normal modes are functionally relevant, but in no case has it been found that the lowest frequency normal mode corresponds exactly to a functional mode. Indeed, one would not expect this to be the case. 

With regard to the comments just made by Professor Somorjai, it may be appropriate to note that some experimental and theoretical evidence does suggest a role for low-frequency, thermal fluctuations in protein structure in enzyme catalysis. 

To investigate the relationship between the reaction driven v7 mode and the subsequent protein motions along the dissociative pathway, further modulations of the frequency of the v7 mode by the surrounding intramolecular and protein bath fluctuations were found using an instantaneous frequency (IF) analysis. The IF was derived from the data by applying a Gaussian filter around the v7 mode in the Fourier spectrum. An inverse Fourier transform produced the time trace TT(t) given by ... 

Solutions of many proteins, synthetic polypeptides, and nucleic acids show large increases in permittivity c (u>) over that of solvent, normally aqueous, at sufficiently low frequencies f = w/2ir of steady state AC measurements, but with dispersion and absorption processes which may lie anywhere from subaudio to megahertz frequencies. Although our interest here is primarily in counterion fluctuation effects as the origin of polarization of aqueous DNA solutions, we first summarize some relevant results of other models for biopolymers. 

In the local mechanical fluctuation model, the local motions of the amino acids on the proximal side of the heme are coupled to the heme through the side group of the proximal histidine. The side chain of the proximal histidine is covalently bonded to the Fe. This bond is the only covalent bond of the heme to the rest of the protein. Thus, motions of the a-helix that contains the proximal histidine are directly coupled the Fe. These motions can push and pull the Fe out of the plane of the heme. Since the CO is bound to the Fe, these motions may induce changes in the CO vibrational transition frequency causing pure dephasing. 

It is evident from these data that the transition frequency fluctuation correlation function of samples that have the same probe molecule (azide) embedded into two different proteins (hemoglobin and carbonic anhydrase), or of the sample with different probe molecules (azide, carbon monoxide) embedded to one protein (hemoglobin), all differ considerably. This, we believe, is a consequence of sensitivity of this spectroscopic technique to the local structure, which is different in each case. This result must be contrasted with electronic dephasing, where it was found that the energy gap fluctuation correlation function reflects the response of the bulk solvent and is essentially independent of the chromophore used as a probe (81). 

We have presented two types of nonlinear IR spectroscopic techniques sensitive to the structure and dynamics of peptides and proteins. While the 2D-IR spectra described in this section have been interpreted in terms of the static structure of the peptide, the first approach (i.e., the stimulated photon echo experiments of test molecules bound to enzymes) is less direct in that it measures the influence of the fluctuating surroundings (i.e., the peptide) on the vibrational frequency of a test molecule, rather than the fluctuations of the peptide backbone itself. Ultimately, one would like to combine both concepts and measure spectral diffusion processes of the amide I band directly. Since it is the geometry of the peptide groups with respect to each other that is responsible for the formation of the amide I excitation band, its spectral diffusion is directly related to structural fluctuations of the peptide backbone itself. A first step to measuring the structural dynamics of the peptide backbone is to measure stimulated photon echoes experiments on the amide I band (51). 

---