Analysis modes

In general, each nomial mode in a molecule has its own frequency, which is detemiined in the nonnal mode analysis [24]- Flowever, this is subject to the constraints imposed by molecular synmietry [18, 25, 26]. For example, in the methane molecule CFI, four of the nonnal modes can essentially be designated as nonnal stretch modes, i.e. consisting primarily of collective motions built from the four C-FI bond displacements. The molecule has tetrahedral synmietry, and this constrains the stretch nonnal mode frequencies. One mode is the totally symmetric stretch, with its own characteristic frequency. The other tliree stretch nonnal modes are all constrained by synmietry to have the same frequency, and are refened to as being triply-degenerate. 

To calculate N (E-Eq), the non-torsional transitional modes have been treated as vibrations as well as rotations [26]. The fomier approach is invalid when the transitional mode s barrier for rotation is low, while the latter is inappropriate when the transitional mode is a vibration. Hamionic frequencies for the transitional modes may be obtained from a semi-empirical model [23] or by perfomiing an appropriate nomial mode analysis as a fiinction of the reaction path for the reaction s potential energy surface [26]. Semiclassical quantization may be used to detemiine anliamionic energy levels for die transitional modes [27]. 

The transfonnation matrix L is obtained from a nonnal-mode analysis perfonned in internal coordmates [59, ]. Thus, as the evolution of the nonnal-mode coordinates versus time is evaluated from equation (A3.12.49), displacements in the internal coordinates and a value for q are found from equation (A3.12.50). The variation in q with time results from a superposition of the nonnal modes. At a particular time, the... 

Minehardt T A, Adcock J D and Wyatt R E 1999 Quantum dynamics of overtone relaxation in 30-mode benzene a time-dependent local mode analysis for CH(v = 2) J. Chem. Phys. 110 3326-34... 

Seeley G and Keyes T 1989 Normal-mode analysis of liquid-state dynamios J. Chem. Phys. 91 5581-6... 

The combination is in this case an out-of-phase one (Section I). This biradical was calculated to be at an energy of 39.6 kcal/mol above CHDN (Table ni), and to lie in a real local minimum on the So potential energy surface. A normal mode analysis showed that all frequencies were real. (Compare with the prebenzvalene intermediate, discussed above. The computational finding that these species are bound moieties is difficult to confimi experimentally, as they are highly reactive.)... 

Hayward, S., Kitao, A., Berendsen, H.J.C. Model-free methods to analyze domain motions in proteins from simulation A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 27 (1997) 425-437. 

The influence of solvent can be incorporated in an implicit fashion to yield so-called langevin modes. Although NMA has been applied to allosteric proteins previously, the predictive power of normal mode analysis is intrinsically limited to the regime of fast structural fluctuations. Slow conformational transitions are dominantly found in the regime of anharmonic protein motion. 

Amadei et al. 1993] Amadei, A., Linssen, A.B.M., Berendsen, H.J.C. Essential Dynamics of Proteins. Proteins 17 (1993) 412-425 [Balsera et al. 1997] Balsera, M., Stepaniants, S., Izrailev, S., Oono, Y., Schiilten, K. Reconstructing Potential Energy Functions from Simulated Force-Induced Unbinding Processes. Biophys. J. 73 (1997) 1281-1287 [Case 1996] Case, D.A. Normal mode analysis of protein dynamics. Curr. Op. Struct. Biol. 4 (1994) 285-290... 

Hayward et al. 1994] Hayward, S., Kitao, A., Go, N. Harmonic and anharmonic aspects in the dynamics of BPTI A normal mode analysis and principal component analysis. Prot. Sci. 3 (1994) 936-943 [Head-Gordon and Brooks 1991] Head-Gordon, T., Brooks, C.L. Virtual rigid body dynamics. Biopol. 31 (1991) 77-100... 

Steven Hayward, Akio Kitao, and Nobuhiro Go. Harmonic and anharmonic aspects in the dynamics of BPTI A normal mode analysis and principal component analysis. Physica Scripta, 3 936-943, 1994. 

D. A. Case. Normal mode analysis of protein dynamics. Curr. Opin. Struc. Biol., 4 385-290, 1994. 

It is also possible to use normal mode analysis [7] to estimate the difference between the exact and the optimal trajectories. Yet another formula is based on the difference between the optimal and the exact actions 2a w [5[Yeract(t)] (f)]]- The action is computed (of course), employ-... 

Energy minimisation and normal mode analysis have an important role to play in the study of the solid state. Algorithms similar to those discussed above are employed but an extra feature of such systems, at least when they form a perfect lattice, is that it is can be possible to exploit the space group symmetry of the lattice to speed up the calculations. It is also important to properly take the interactions with atoms in neighbouring cells into account. 

A particular advantage of the low-mode search is that it can be applied to botli cyclic ajic acyclic molecules without any need for special ring closure treatments. As the low-mod> search proceeds a series of conformations is generated which themselves can act as starting points for normal mode analysis and deformation. In a sense, the approach is a system ati( one, bounded by the number of low-frequency modes that are selected. An extension of th( technique involves searching random mixtures of the low-frequency eigenvectors using Monte Carlo procedure. 

Once the 3D strucmre of a molecule and all the parameters required for the atomic and molecular connectivities are known, the energy of the system can be calculated via Eqs. (l)-(3). First derivatives of the energy with respect to position allow for determination of the forces acting on the atoms, information that is used in the energy minimization (see Chapter 4) or MD simulations (see Chapter 3). Second derivatives of the energy with respect to position can be used to calculate force constants acting on atoms, allowing the determination of vibrational spectra via nonnal mode analysis (see Chapter 8). 

More traditional applications of internal coordinates, notably normal mode analysis and MC calculations, are considered elsewhere in this book. In the recent literature there are excellent discussions of specific applications of internal coordinates, notably in studies of protein folding [4] and energy minimization of nucleic acids [5]. 

Normal mode analysis exists as one of the two main simulation techniques used to probe the large-scale internal dynamics of biological molecules. It has a direct connection to the experimental techniques of infrared and Raman spectroscopy, and the process of comparing these experimental results with the results of normal mode analysis continues. However, these experimental techniques are not yet able to access directly the lowest frequency modes of motion that are thought to relate to the functional motions in proteins or other large biological molecules. It is these modes, with frequencies of the order of 1 cm , that mainly concern this chapter. 

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. 

In the following, the method itself is introduced, as are the various techniques used to perform normal mode analysis on large molecules. The method of normal mode refinement is described, as is the place of normal mode analysis in efforts to characterize the namre of a protein s conformational energy surface. 

II. NORMAL MODE ANALYSIS IN CARTESIAN COORDINATE SPACE... 

This section describes the basic methodology of normal mode analysis. Owing to its long history it has been described in detail in the context of many different fields. However, to aid in understanding subsequent sections of this chapter, it is described here in some detail. 

III. NORMAL MODE ANALYSIS OF LARGE BIOLOGICAL MOLECULES... 

B. Normal Mode Analysis in Dihedral Angle Space... 

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