Order parameter complex

An advantage of NMR spectroscopy is the analysis of protein dynamics. Measurement and analysis of the relaxation parameters R1 R2, and the 15N NOE of 15N-labeled proteins leads to an order parameter (S2) that can describe the relative mobility of the backbone of the protein. Both collagenase-1 and stromelysin-1 have been studied either as inhibited complexes or the free protein [19, 52], Stromleysin-1 was studied with inhibitors binding to prime or nonprime subsites. Presence or absence of inhibitors in the nonprime sites had minor effects on the highly ordered structure of residues in these subsites, which are in contact with the... 

Although the underlying physics and mathematics used to convert relaxation rates into molecular motions are rather complex (Lipari and Szabo, 1982), the most important parameter obtained from such analyses, the order parameter. S 2, has a simple interpretation. In approximate terms, it corresponds to the fraction of motion experienced by a bond vector that arises from slow rotation as a rigid body of roughly the size of the macromolecule. Thus, in the interior of folded proteins, S2 for Hn bonds is always close to 1.0. In very flexible loops, on the other hand, it may drop as low as 0.6 because subnanosecond motions partially randomize the bond vector before it rotates as a rigid body. 

In this simple model characterized by a single scalar order parameter, the structures with periodic surfaces are metastable. It simply means that we need a more complex model including the surfactant degrees of freedom (its polar nature) in order to stabilize structures with P, D, and G surfaces. In the Ciach model [120-122] indeed the introduction of additional degrees of freedom stabilizes such structures. 

Biological membranes fluidity order parameters lipid-protein interactions translational diffusion site accessibility structural changes membrane potentials complexes and binding energy-linked and light-induced changes effects of additives location of proteins lateral organization and dynamics... 

Most of the experimental results on CJTE can be explained on the basis of molecular field theory. This is because the interaction between the electron strain and elastic strain is fairly long-range. Employing simple molecular field theory, expressions have been derived for the order parameter, transverse susceptibility, vibronic states, specific heat, and elastic constants. A detailed discussion of the theory and its applications may be found in the excellent review by Gehring Gehring (1975). In Fig. 4.23 various possible situations of different degrees of complexity that can arise in JT systems are presented. 

We assume the system under consideration to be a single domain. Then the orientational state of the system can be specified by the order parameter tensor S defined by Eq. (63), The time evolution of S is governed by the kinetic equation, Eq. (64), along with Eqs. (62) and (65). This kinetic equation tells us that the orientational state in the rodlike polymer system in an external flow field is determined by the term F related to the mean-field potential Vscf and by the term G arising from the external flow field. These two terms control the orientation state in a complex manner as explained below. 

I think Dr. Williams avowed pessimism is inevitable if one is trying to explain all biological phenomena in terms of molecular, microscopic concepts. But molecular description can be a Procrustean bed when dealing with complex, intrinsically macroscopic phenomena, because simple interpretability may not be feasible. In fact, the selection of a few essential macroscopic variables from a vast number of microscopic variables (or their combinations) is crucial not only for understanding via simplification, but also because collective variables (order parameters) tend to obey qualitatively different rules or laws that are not obvious in,... 

---