Enzymes protein motion effects

Because both the passive fluctuations and the modulating vibrations can require thermal excitation, this model is capable of accounting for temperature-dependent isotope effects, including those traditionally described by the BeU model. Theoretical studies, which will be the topic of the second and third parts of this three-part series of articles, have not yet produced a consensus on the contribution of specific protein motions to enzyme catalysis. 

Many of these changes In membrane fatty acid composition probably act by modulating enzymic activity by regulating localized or bulk membrane fluidity however, since most studies have not measured rates or ranges of lipid or protein motion as a function of changes In fatty acid composition, or even differentiated between total cell and phospholipid composition, there Is little direct support for this hypothesis. An additional complication Is the possible presence of laterally segregated lipid domains which could have profound effects on protein assembly or enzyme activity with minimal changes In bulk membrane fluidity. 

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. 

Another important area of dynamic studies in biological samples is the effect of hydration upon molecular mobility in proteins and carbohydrates. The reason for these studies is primarily that protein dynamics, in particular, are crucial to their function, and so examining factors, such as the degree of hydration, that affect their dynamics is very important. However, it is obviously near-impossible to study dynamics in aqueous solution as a function of degree of hydration, and, since most proteins are not soluble in nonaqueous solvents, solid-state studies must be used. The motions at three methionine (Met) residues in Streptomyces subtilisin inhibitor (SSI) were studied with 2H NMR using a sample in which the Met residues at two crucial enzyme recognition sites (PI and P4) were specifically deuterated, along with one in the hydrophobic core.114 The motions of the Met side-chains were then examined... 

Although biologic membranes serve as physical barriers, it is important to recognize that their molecular constituents are in a constant state of motional flux. Many different types of molecular motion are present in biological membranes including rotation, translation and libration, each of which contributes in important ways to the physical properties of cellular membranes. Since alterations in membrane physical properties have profound effects on the kinetics of many transmembrane enzymes and modulate the rates and types of interactions between proteins, it comes as no surprise that the molecular dynamics of a cell membrane is an important modulator of signal transduction (e.g., Lenaz, 1987). Thus, biological... 

Finally, another critical aspect for rapid and predictive design is the lack of information available about the dynamics of these enzymatic systems. Prediction of the effect of a mutation on the enzyme structure and dynamics remains a difficult task. Molecular dynamics and simulations of protein and substrate motions combined with the use of biophysical techniques enabling conformational changes to be trapped have to be developed. Multidisciplinary approaches will undoubtedly lead to major advances in this field and help to promote the key role that computational methods must play for efficient re-engineering of enzymes. These new ways to accelerate the evolution process and identify mutation sites important for optimizing enzyme characteristics will help to provide rapidly a well-expressed, efficient, stable, and specific enzyme, in other words the ideal glucansucrase for biocatalysis. 

---