Proteins time scale, motions

Protein dynamics occurs on very different time scales ([McCammon and Harvey 1987, Jardetzky 1996]). Here, we are most interested in long time scale motions such as relative motion between secondary structure elements, and inter-domain motion. 

In contrast to Ri, R2, and N- H] NOE experiments that characterize subnanosecond motions, CPMG and spin-lock relaxation experiments provide quantitative information about mUli- to microsecond time scale motions. In this section, the relaxation dispersion is first defined, and, subsequently, CPMG and spin-lock / 2 dispersion experiments that have recently been developed for applications to proteins are reviewed. 

Ishima R, Wingfield PT, Stahl SJ, Kaufman JD, Torchia DA (1998) Using amide H-1 and N-15 transverse relaxation to detect millisecond time-scale motions in perdeuterated proteins application to HIV-1 protease. J Am Chem Soc 120 10534-10542... 

Genberg L, Richard L, McLendon G and Miller R J D 1991 Direct observation of global protein motion in hemoglobin and myoglobin on picosecond time scales Science 251 1051-6... 

The simulations also revealed that flapping motions of one of the loops of the avidin monomer play a crucial role in the mechanism of the unbinding of biotin. The fluctuation time for this loop as well as the relaxation time for many of the processes in proteins can be on the order of microseconds and longer (Eaton et al., 1997). The loop has enough time to fluctuate into an open state on experimental time scales (1 ms), but the fluctuation time is too long for this event to take place on the nanosecond time scale of simulations. To facilitate the exit of biotin from its binding pocket, the conformation of this loop was altered (Izrailev et al., 1997) using the interactive molecular dynamics features of MDScope (Nelson et al., 1995 Nelson et al., 1996 Humphrey et al., 1996). 

Molecular dynamics simulations ([McCammon and Harvey 1987]) propagate an atomistic system by iteratively solving Newton s equation of motion for each atomic particle. Due to computational constraints, simulations can only be extended to a typical time scale of 1 ns currently, and conformational transitions such as protein domains movements are unlikely to be observed. 

The first term represents the forces due to the electrostatic field, the second describes forces that occur at the boundary between solute and solvent regime due to the change of dielectric constant, and the third term describes ionic forces due to the tendency of the ions in solution to move into regions of lower dielectric. Applications of the so-called PBSD method on small model systems and for the interaction of a stretch of DNA with a protein model have been discussed recently ([Elcock et al. 1997]). This simulation technique guarantees equilibrated solvent at each state of the simulation and may therefore avoid some of the problems mentioned in the previous section. Due to the smaller number of particles, the method may also speed up simulations potentially. Still, to be able to simulate long time scale protein motion, the method might ideally be combined with non-equilibrium techniques to enforce conformational transitions. 

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

As an example for an efficient yet quite accurate approximation, in the first part of our contribution we describe a combination of a structure adapted multipole method with a multiple time step scheme (FAMUSAMM — fast multistep structure adapted multipole method) and evaluate its performance. In the second part we present, as a recent application of this method, an MD study of a ligand-receptor unbinding process enforced by single molecule atomic force microscopy. Through comparison of computed unbinding forces with experimental data we evaluate the quality of the simulations. The third part sketches, as a perspective, one way to drastically extend accessible time scales if one restricts oneself to the study of conformational transitions, which arc ubiquitous in proteins and are the elementary steps of many functional conformational motions. 

The previous application — in accord with most MD studies — illustrates the urgent need to further push the limits of MD simulations set by todays computer technology in order to bridge time scale gaps between theory and either experiments or biochemical processes. The latter often involve conformational motions of proteins, which typically occur at the microsecond to millisecond range. Prominent examples for functionally relevant conformatiotial motions... 

Fig. 10. Conformational flooding accelerates conformational transitions and makes them accessible for MD simulations. Top left snapshots of the protein backbone of BPTI during a 500 ps-MD simulation. Bottom left a projection of the conformational coordinates contributing most to the atomic motions shows that, on that MD time scale, the system remains in its initial configuration (CS 1). Top right Conformational flooding forces the system into new conformations after crossing high energy barriers (CS 2, CS 3,. . . ). Bottom right The projection visualizes the new conformations they remain stable, even when the applied flooding potentials (dashed contour lines) is switched off.

Since NMR relaxation in proteins is determined by dynamics on the picosecond to nanosecond time scale, experimental NMR relaxation parameters can provide important information concerning picosecond motions. Time correlation func-... 

For folded proteins, relaxation data are commonly interpreted within the framework of the model-free formalism, in which the dynamics are described by an overall rotational correlation time rm, an internal correlation time xe, and an order parameter. S 2 describing the amplitude of the internal motions (Lipari and Szabo, 1982a,b). Model-free analysis is popular because it describes molecular motions in terms of a set of intuitive physical parameters. However, the underlying assumptions of model-free analysis—that the molecule tumbles with a single isotropic correlation time and that internal motions are very much faster than overall tumbling—are of questionable validity for unfolded or partly folded proteins. Nevertheless, qualitative insights into the dynamics of unfolded states can be obtained by model-free analysis (Alexandrescu and Shortle, 1994 Buck etal., 1996 Farrow etal., 1995a). An extension of the model-free analysis to incorporate a spectral density function that assumes a distribution of correlation times on the nanosecond time scale has recently been reported (Buevich et al., 2001 Buevich and Baum, 1999) and better fits the experimental 15N relaxation data for an unfolded protein than does the conventional model-free approach. 

The QM/MM and ab initio methodologies have just begun to be applied to challenging problems involving ion channels [73] and proton motion through them [74]. Reference [73] utilizes Hartree-Fock and DFT calculations on the KcsA channel to illustrate that classical force fields can fail to include polarization effects properly due to the interaction of ions with the protein, and protein residues with each other. Reference [74] employs a QM/MM technique developed in conjunction with Car-Parrinello ab initio simulations [75] to model proton and hydroxide ion motion in aquaporins. Due to the large system size, the time scale for these simulations was relatively short (lOps), but the influences of key residues and macrodipoles on the short time motions of the ions could be examined. 

Which model provides the best representation for local mobility in a particular group remains unclear, as a detailed picture of protein dynamics is yet to be painted. This information is not directly available from NMR measurements that are necessarily limited by the number of experimentally available parameters. Additional knowledge is required in order to translate these experimental data into a reliable motional picture of a protein. At this stage, molecular dynamic simulations could prove extremely valuable, because they can provide complete characterization of atomic motions for all atoms in a molecule and at all instants of the simulated trajectory. This direction becomes particularly promising with the current progress in computational resources, when the length of a simulated trajectory approaches the NMR-relevant time scales [23, 63, 64]. 

The major reasons for using intrinsic fluorescence and phosphorescence to study conformation are that these spectroscopies are extremely sensitive, they provide many specific parameters to correlate with physical structure, and they cover a wide time range, from picoseconds to seconds, which allows the study of a variety of different processes. The time scale of tyrosine fluorescence extends from picoseconds to a few nanoseconds, which is a good time window to obtain information about rotational diffusion, intermolecular association reactions, and conformational relaxation in the presence and absence of cofactors and substrates. Moreover, the time dependence of the fluorescence intensity and anisotropy decay can be used to test predictions from molecular dynamics.(167) In using tyrosine to study the dynamics of protein structure, it is particularly important that we begin to understand the basis for the anisotropy decay of tyrosine in terms of the potential motions of the phenol ring.(221) For example, the frequency of flips about the C -C bond of tyrosine appears to cover a time range from milliseconds to nanoseconds.(222)... 

Recent results show large variations in intramolecular rotations of tryptophan residues in proteins on the nanosecond time scale, ranging from complete absence of mobility to motions of considerable angular amplitudes. Among native proteins with internal tryptophan residues, wide angular amplitude rotations were observed only in studies of azurin,(28 29) where the correlation time of the rapid component was x = 0.51 ns.(28) The existence of... 

The results obtained show that the dipole-relaxational motions in protein molecules are really very retarded as compared to such motions in the environment of aromatic molecules dissolved in liquid solvents (where they occur on a time scale of tens of picoseconds).(82) Dipole-relaxational motions on the nanosecond time scale have been observed for a variety of proteins. For example, such motions were recorded for apohemoglobin and bovine serum albumin0 04 105) labeled with the fluorescent probe 2,6-TNS. 

Thus, at present, fluorescence spectroscopy is capable of providing direct information on molecular dynamics on the nanosecond time scale and can estimate the results of dynamics occurring beyond this range. The present-day multiparametric fluorescence experiment gives new opportunities for interpretation of these data and construction of improved dynamic models. A further development of the theory which would provide an improved description of the dynamics in quantitative terms with allowance for the structural inhomogeneity of protein molecules and the hierarchy of their internal motions is required. 

The properties of membranes commonly studied by fluorescence techniques include motional, structural, and organizational aspects. Motional aspects include the rate of motion of fatty acyl chains, the head-group region of the phospholipids, and other lipid components and membrane proteins. The structural aspects of membranes would cover the orientational aspects of the lipid components. Organizational aspects include the distribution of lipids both laterally, in the plane of the membrane (e.g., phase separations), and across the membrane bilayer (phospholipid asymmetry) and distances from the surface or depth in the bilayer. Finally, there are properties of membranes pertaining to the surface such as the surface charge and dielectric properties. Fluorescence techniques have been widely used in the studies of membranes mainly since the time scale of the fluorescence lifetime coincides with the time scale of interest for lipid motion and since there are a wide number of fluorescence probes available which can be used to yield very specific information on membrane properties. 

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