Protein thermal motion

Effect of Temperature and pH. The temperature dependence of enzymes often follows the rule that a 10°C increase in temperature doubles the activity. However, this is only tme as long as the enzyme is not deactivated by the thermal denaturation characteristic for enzymes and other proteins. The three-dimensional stmcture of an enzyme molecule, which is vital for the activity of the molecule, is governed by many forces and interactions such as hydrogen bonding, hydrophobic interactions, and van der Waals forces. At low temperatures the molecule is constrained by these forces as the temperature increases, the thermal motion of the various regions of the enzyme increases until finally the molecule is no longer able to maintain its stmcture or its activity. Most enzymes have temperature optima between 40 and 60°C. However, thermostable enzymes exist with optima near 100°C. 

An approach to overcome the multi minima problem of proteins is simulated annealing (SA) run. Besides global molecular properties such as structural and thermal motions, functional properties of fast biological reactions can also be studied by MD. 

Vibrational spectroscopy has played a very important role in the development of potential functions for molecular mechanics studies of proteins. Force constants which appear in the energy expressions are heavily parameterized from infrared and Raman studies of small model compounds. One approach to the interpretation of vibrational spectra for biopolymers has been a harmonic analysis whereby spectra are fit by geometry and/or force constant changes. There are a number of reasons for developing other approaches. The consistent force field (CFF) type potentials used in computer simulations are meant to model the motions of the atoms over a large ranee of conformations and, implicitly temperatures, without reparameterization. It is also desirable to develop a formalism for interpreting vibrational spectra which takes into account the variation in the conformations of the chromophore and surroundings which occur due to thermal motions. 

Studies of the effect of permeant s size on the translational diffusion in membranes suggest that a free-volume model is appropriate for the description of diffusion processes in the bilayers [93]. The dynamic motion of the chains of the membrane lipids and proteins may result in the formation of transient pockets of free volume or cavities into which a permeant molecule can enter. Diffusion occurs when a permeant jumps from a donor to an acceptor cavity. Results from recent molecular dynamics simulations suggest that the free volume transport mechanism is more likely to be operative in the core of the bilayer [84]. In the more ordered region of the bilayer, a kink shift diffusion mechanism is more likely to occur [84,94]. Kinks may be pictured as dynamic structural defects representing small, mobile free volumes in the hydrocarbon phase of the membrane, i.e., conformational kink g tg ) isomers of the hydrocarbon chains resulting from thermal motion [52] (Fig. 8). Small molecules can enter the small free volumes of the kinks and migrate across the membrane together with the kinks. 

These studies provide the first advanced EPR studies of a non-Kramers doublet spin system, and they suggest the possibility of investigating similar signals from other proteins in this family. EXAFS spectroscopy does not exhibit Fe- -Fe backscattering in Hred (38). This observation could reflect thermal motion, or it may suggest that, as a consequence of the reduction of Hox to Hred, the Fe-Fe distance has... 

A number of transport mediators are transport proteins in the absence of an external energy supply, thermal motion leads to their conformational change or rotation so that the transported substance, bound at one side of the membrane, is transferred to the other side of the membrane. This type of mediator has a limited number of sites for binding the transported substance, so that an increase in the concentration of the latter leads to saturation. Here, the transport process is characterized by specificity for a given substance and inhibition by other transportable substances competing for binding sites and also by various inhibitors. When the concentrations of the transported substance are identical on both sides of the membrane,... 

Although the stabilizing interactions between the amino acid side chains of PLC/j, and the choline headgroup are readily apparent in the PLC fc-phosphonate inhibitor complex, it is more difficult to identify contacts between the protein and the acyl chains of the inhibitor [45]. In part this is because thermal motion in the acyl side chains, especially the sn-1 chain, renders them somewhat disordered. Consequently, the measured distances between the side chain carbons... 

Burling, F. T. and Brunger, A. T. (1994) Thermal motion and conformational disorder in protein crystal structures. Isr. J. Chem. 34,165-175. 

In crystal structure analyses of proteins, the presence of Ca ions is usually determined indirectly. Ions, being larger and more electron dense, are differentiated from water molecules based on their peak heights in electron density maps, and their high occupancies and low thermal motion parameters during least-squares refinement of the... 

An x-ray analysis will measure the diffraction pattern (positions and intensities) and the phases of the waves that formed each spot in the pattern. These parameters combined result in a three-dimensional image of the electron clouds of the molecule, known as an electron density map. A molecular model of the sequence of amino acids, which must be previously identified, is fitted to the electron density map and a series of refinements are performed. A complication arises if disorder or thermal motion exist in areas of the protein crystal this makes it difficult or impossible to discern the three-dimensional structure (Perczel et al. 2003). 

In the preceding Section (5.3) the CD bands in the near ultraviolet region are assigned to those of tyrosyl and phenylalanyl residues, whose thermal motions are restricted sterically keeping their geometry constant around the main chain in the proteins. The CD spectrum of aromatic moieties provides a good measure for the analysis of motional freedom around a given amino acid residue. Better examples have been reported on several kinds of amino acids and their polymers. 

Occupancies rij for atoms of the protein (but not necessarily its ligands, which may be present at lower occupancies) are usually constrained at 1.0 early in refinement, and in many refinements are never released, so that both thermal motion and disorder show their effects upon the final B values. In some cases, after refinement converges, a few B values fall far outside the average range for the model. This is sometimes an indication of disorder. Careful examination of 2Fq— Fc and FQ— Fc maps may give evidence for more than one conformation in such a troublesome region. If so, inclusion of multiple conformations followed by refinement of their occupancies may improve the R-factor and the map, revealing the nature of the disorder more clearly. 

The range of application of the three pressure-driven membrane water separation processes—reverse osmosis, ultrafiltration and microfiltration—is illustrated in Figure 1.2. Ultrafiltration (Chapter 6) and microfiltration (Chapter 7) are basically similar in that the mode of separation is molecular sieving through increasingly fine pores. Microfiltration membranes filter colloidal particles and bacteria from 0.1 to 10 pm in diameter. Ultrafiltration membranes can be used to filter dissolved macromolecules, such as proteins, from solutions. The mechanism of separation by reverse osmosis membranes is quite different. In reverse osmosis membranes (Chapter 5), the membrane pores are so small, from 3 to 5 A in diameter, that they are within the range of thermal motion of the polymer... 

To elucidate the role ofhydrophobic bonding, a detailed study on the kinetics ofin-testinal absorption has been performed on sulfonamides. It was concluded that transport across the microvillus membrane occurs via kinks in the membrane which are pictured as mobile structural defects representing mobile free volumes in the hydrocarbon phase of the membrane and whose diffusion coefficient is fairly fast ( 10-5 cm2/s) [1]. The thermal motion of the hydrocarbon chain leads to the formation of kinks. It was also postulated that a transient association of the drug molecules with proteins on the surface of the microvillus membrane is involved in the formation of the activated complex in the absorption process [1]. 

As already pointed out in Part III, Chapter 19, in the crystal structures of proteins the amino acid main-chain and side-chain atoms at the periphery of the molecule display larger thermal motion (associated with larger B-factors [A2]) than those in the interior. Since the water of hydration molecules are bound primarily to these peripheral protein atoms, they display similar, and in general even more excessive thermal motion. As a consequence, the interpretation of the hydration water structure can be ambiguous, as outlined in Box 23.1. 

Hydration of an alanine side-chain. In human lysozyme, the methyl group of Ala92 is surrounded by four water molecules located on a semi-circle ([625], Fig. 23.6). These hydration waters are buried in the protein which might be the reason why they are so well ordered. We can also assume that such hydration schemes occur at the protein periphery but they are not seen in the X-ray analyses due to larger-thermal motion and/or disorder of the water molecules. 

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