ScienceWeek

BIOCHEMISTRY: ON PROTEIN DYNAMICS

The following points are made by Michel Orrit (Science 2003 302:239):

1) Proteins are not static. Conformational flexibility at various levels of their hierarchical structure enables proteins to fulfill a wide range of complex biological functions. Most proteins are highly complex macromolecules (2). Driven by Brownian motion, they wander in an intricate multidimensional energy landscape, featuring multitudes of interconnected wells and dells, valleys and passes. Hopping from well to well can be as fast as tens of femtoseconds for fast backbone vibrations, or as slow as hours and even days for folding and maturation in large proteins -- a range of time scales spanning 18 orders of magnitude. To make matters worse, protein functions such as catalytic reactions are determined by short-range atom-atom interactions and critically depend on tiny atomic displacements. Understanding of such subtlety and complexity is still in its infancy. Numerical simulations (3) can handle ever more complexity, but the longest simulations do not exceed a few nanoseconds. Moreover, computations must eventually be compared with experiments.

2) Current experiments to explore protein dynamics are of two kinds. First, fluctuation amplitudes may be measured with a range of techniques, each of which has a characteristic time window. The diffraction of x-rays and neutrons falls into this group, as do various spectroscopies, including nuclear or electronic magnetic resonance (4,5), Mössbauer absorption, infrared, and Raman spectroscopy. NMR is particularly powerful because it can distinguish each amino acid residue in the sequence, but it does not cover all fluctuation time scales.

3) Second, an ensemble of molecules may be synchronously brought out of equilibrium, and its subsequent relaxation monitored as a function of time. The initial disturbance in such kinetic measurements can be a temperature jump, a sudden concentration change, or -- on much shorter time scales -- the breaking of a bond by a laser pulse. Under such strong perturbations, however, proteins may no longer be close to equilibrium. Furthermore, synchronization is short-lived. Because different individual molecules follow different pathways in the energy landscape, subsequent events occur over an ever wider range of delays.

4) Single-molecule methods overcome the latter difficulty. Like an orchestra, a molecular ensemble needs to be synchronized for the outcome to be comprehensible. In contrast, a single molecule is a soloist, directly imparting its intricate improvisations to us. The pathway it takes can, in principle, be tracked as a function of time, allowing rare and potentially crucial events to be captured under physiological conditions and at equilibrium.(1)s

References (abridged):

1. H. Yang et al., Science 302, 262 (2003)

2. H. Frauenfelder et al., Science 254, 1598 (1991)

3. R. A. Böckmann, H. Grubmüller, Nature Struct. Biol. 9, 198 (2002)

4. R. Ishima, D. A. Torchia, Nature Struct. Biol. 7, 740 (2000)

5. L. Columbus, W. L. Hubbell, Trends Biochem. Sci. 27, 288 (2002)

Science http://www.sciencemag.org

ScienceWeek http://www.scienceweek.com