SOME PROTEIN PROPERTIES IMPORTANT FOR ENZYME CATALYSIS - New Trends in Enzyme Catalysis and Biomimetic Chemical Reactions - page 142

al., 2001). The buried water molecules in hydrophobic pores and in superficial clefts are
measured on a nanosecond time scale, while sub-nanosecond correlation time is
characteristic of surface hydration water.
All theoretical results for protein and solvent dynamics mentioned above agree with
experimental data obtained earlier by physical methods and biophysical labeling
methods, in particular).

4.1.6. MECHANISMS OF PROTEINS MOLECULAR DYNAMICS

Data on the intramolecular dynamics of proteins obtained by the physical labeling
approach combined with other dynamical and complementary theoretical and
experimental methods may be briefly summarized as follows.
1. At low temperatures and in dry samples, protein macromolecules exhibit high
frequency low amplitude harmonic nuclear vibrations with and

amplitude A = 0.01 - 0.05 . This type of motion, directly detected by the methods of

IR, Raman, Mössbauer, NMR and ESR spectroscopy, takes place in all proteins, at all
temperatures and degrees of humidity, and apparently is not directly related to their
functions and stability.
2. Anharmonic low frequency

Å

and relatively high amplitude

.and more) appear at certain critical temperatures, 180 - 210 K, and
degree hydration (10- 30%) depending on protein structure. Protein conformational
flexibility in the nanosecond and subnanosecond time scale was revealed in experiments
on the fluorescence quenching of the buried tryptophane residues (Lakowicz and Weber,
1973; Munro et al., 1979), time-resolved tryptophane fluorescence by time- resolved
fluorescence (Nishimoto et al., 1998), and spin, fluorescence and Mössbauer labelling
(Likhtenshtein, 1976a, b, 1979, 1988, 1993; Likhtenshtein et al., 2000; Parak et al.,
1982; Vogel et al., 1994), neutron and scattering (Tsai et al., 2000; Tarek et al.,
2000), NMR (Kay, 1989; Buck et al., 1995; Shaw et al., 1995; Palmer et al., 1996; Hill
et al., 2001) and in theoretical molecular dynamics simulation (Karplus and McCammon,
1986; Karplus and Petsko, 1990; Zhou et al., 1998; Smith et al., 1998). These motions
are governed by dynamics of media which provide necessary free volume (Lumry and
Rajender, 1970; Lumry and Gregory, 1974, Likhtenhtein, 1969; 1976a, b, 1988).
3. The comparative analysis of the data obtained (Likhteshtein, 1976a, b, 1979, 1988;
Likhtenshtein et al., 2000) revealed an apparent discrepancy between the physical
labeling approach and certain other physical methods. Thus, the measurements of the
temperature dependence of the heat capacity of proteins, lysozyme,
myoglobin, collagen, etc. at T 180-210 K at various degrees of hydration indicated only
a monotonic increase of and did not detect pronounced phase transitions (Privalov
aand Gill, 1998; 1982; Realdi and Battisel, 1993; Battisel et al., 2000). However, spin,
fluorescence and Mössbauer labelling, H-D exchange, non-elastic neutron scattering and
absorption spectra of heme in heme proteins detected sharp transitions within this
temperature range. Parallel results were confirmed in experiments on the T-dependencies
of such physical parameters of proteins as heat capacitiy and circular dichroism at the
physiological temperature interval before thermal denaturation.

motions (0.2 Å