Conformational state

Warshaw D M, Hayes E, Gaffney D, Lauzon A-M, Wu J, Kennedy G, Trybus K, Lowey S and Berger C 1998 Myosin conformational states determined by single fluorophore polarization Proc. Natl Acad. Sc/. USA 95 8034-9... 

We consider a finite space, which contains the NA sample and is in contact with a bath of water or water vapor. That allows one to maintain the r.h. in the experimental space at a constant level and change it when necessary. Such a scheme corresponds to the real experiments with wet NA samples. A NA molecule is simulated by a sequence of units of the same type. Thus, in the present study, we consider the case of a homogeneous NA or the case where averaging over the unit type is possible. Every unit can be found in the one of three conformational states unordered. A- or B- conformations. The units can reversibly change their conformational state. A unit corresponds to a nucleotide of a real NA. We assume that the NA strands do not diverge during conformational transitions in the wet NA samples [18]. The conformational transitions are considered as cooperative processes that are caused by the unfavorable appearance of an interface between the distinct conformations. 

Let us introduce the variables which are the probabilities of finding an arbitrary nnit in a certain conformational state U for unordered state, A for A- and B for B-form of the NA. There is the natural relationship between the variables ... 

The NAs such as DNA usually used in the experiments consist of 10" -1 o nucleotides. Thus, they should be considered as macrosystems. Moreover, in experiments with wet NA samples macroscopic quantities are measured, so averaging should also be performed over all nucleic acid molecules in the sample. These facts justify the usage of the macroscopic equations like (3) in our case and require the probabilities of finding macromolecular units in the certain conformational state as variables of the model. 

Fiber, R. Karplus, M. Multiple conformational states of proteins a molecular dynamics analysis of myoglobin. Science 235 318-321, 1987. 

Reduce stress on molecules caused by a simulation at elevated temperatures. The cooling process, called simulated annealing, takes new, high energy conformational states toward stable conform ations. 

The ability of receptors to couple to G-proteins and initiate GTPase activity may also be independent of ligand. Thus, specific mutations in a- and P-adrenergic receptors have led to receptors that mediate agonist-independent activation of adenylyl cyclase (69,70). These mutations presumably mimic the conformational state of the ligand-activated receptor when they are activated conventionally by ligands. 

The subunits can switch between two distinct conformational states, R and T, which are in equilibrium. 

Fi re 12.6 Schematic diagram Illustrating the proton movements in the photocycle of bacteriorhodopsin. The protein adopts two main conformational states, tense (T) and relaxed (R). The T state binds trans-tetinal tightly and the R state binds c/s-retinal. (a) Stmcture of bacteriorhodopsin in the T state with hflus-retinal bound to Lys 216 via a Schiff base, (b) A proton is transferred from the Schiff base to Asp 85 following isomerization of retinal and a conformational change of the protein. 

Christian Anfmsen s experiments demonstrated that proteins can fold reversibly. A corollary result of Anfmsen s work is that the native structures of at least some globular proteins are thermodynamically stable states. But the matter of how a given protein achieves such a stable state is a complex one. Cyrus Levinthal pointed out in 1968 that so many conformations are possible for a typical protein that the protein does not have sufficient time to reach its most stable conformational state by sampling all the possible conformations. This argument, termed Levinthal s paradox, goes as follows consider a protein of 100 amino acids. Assume that there are only two conformational possibilities per amino acid, or = 1.27 X 10 ° possibilities. Allow 10 sec for... 

Implicit in the presumption of folding pathways is the existence of intermediate, partially folded conformational states. The notion of intermediate states on the pathway to a tertiary structure raises the possibility that segments of a protein might independently adopt local and well-defined secondary structures (a-helices and /3-sheets). The tendency of a peptide segment to prefer a particular secondary structure depends in turn on its amino acid composition and sequence. 

In 1965, Jacques Monod, Jeffries Wyman, and Jean-Pierre Changeux proposed a theoretical model of allosteric transitions based on the observation that allosteric proteins are oligomers. They suggested that allosteric proteins can exist in (at least) two conformational states, designated R, signifying relaxed, and T, or taut, and that, in each protein molecule, all of the subunits have the same conformation (either R or T). That is, molecular symmetry is conserved. Molecules of mixed conformation (having subunits of both R and T states) are not allowed by this model. 

FIGURE 15.9 Monod-Wyman-Changeux (MWC) model for allosteric transitions. Consider a dimeric protein that can exist in either of two conformational states, R or T. Each subunit in the dimer has a binding site for substrate S and an allosteric effector site, F. The promoters are symmetrically related to one another in the protein, and symmetry is conserved regardless of the conformational state of the protein. The different states of the protein, with or without bound ligand, are linked to one another through the various equilibria. Thus, the relative population of protein molecules in the R or T state is a function of these equilibria and the concentration of the various ligands, substrate (S), and effectors (which bind at f- or Fj ). As [S] is increased, the T/R equilibrium shifts in favor of an increased proportion of R-conformers in the total population (that is, more protein molecules in the R conformational state). 

The Oxy and Deoxy Forms of Hemoglobin Represent Two Different Conformational States... 

A model for the allosteric behavior of hemoglobin is based on recent observations that oxygen is accessible only to the heme groups of the a-chains when hemoglobin is in the T conformational state. Perutz has pointed out that the heme environment of /3-chains in the T state is virtually inaccessible because of steric hindrance by amino acid residues in the E helix. This hindrance dis-... 

AbouKhair, N. K., Ziegler, M. M., and Baldwin, T. O. (1985). Bacterial luciferase demonstration of a catalytically competent altered conformational state following a single turnover. Biochemistry 24 3942-3947. 

As revealed by IR-spectroscopy, the attachment of the polymer proceeds via acylation of aminopropyls absorbances of both amides (1650 cm-1) and esters (1740 cm-1) contribute to the spectrum of polyacrylate-coated aminopropyl-Aerosil (specific surface area 175 m2/g) [55], During the reaction, the accumulation of p-nitrophenyl ester groups in the support is accompanied by the liberation of p-nitrophenol into the contacting solution. Thus, the evaluation of the conformational state of adsorbing macromolecules can be performed by the simultaneous study of both processes by UV-spectroscopy as shown in Fig. 7. Apparently, at... 

The catalytic cycle of the Na+/K+-ATPase can be described by juxtaposition of distinct reaction sequences that are associated with two different conformational states termed Ei and E2 [1]. In the first step, the Ei conformation is that the enzyme binds Na+ and ATP with very high affinity (KD values of 0.19-0.26 mM and 0.1-0.2 pM, respectively) (Fig. 1A, Step 1). After autophosphorylation by ATP at the aspartic acid within the sequence DKTGS/T the enzyme occludes the 3 Na+ ions (Ei-P(3Na+) Fig. la, Step 2) and releases them into the extracellular space after attaining the E2-P 3Na+ conformation characterized by low affinity for Na+ (Kq5 = 14 mM) (Fig. la, Step 3). The following E2-P conformation binds 2 K+ ions with high affinity (KD approx. 0.1 mM Fig. la, Step 4). The binding of K+ to the enzyme induces a spontaneous dephosphorylation of the E2-P conformation and leads to the occlusion of 2 K+ ions (E2(2K+) Fig. la, Step 5). Intracellular ATP increases the extent of the release of K+ from the E2(2K+) conformation (Fig. la, Step 6) and thereby also the return of the E2(2K+) conformation to the EiATPNa conformation. The affinity ofthe E2(2K+) conformation for ATP, with a K0.5 value of 0.45 mM, is very low. 

The Na+/K+-ATPase is the only enzyme known to interact with CTS, which reversibly bind to the extracellular side of the Na+/K+-ATPase at the E2-P conformational state [E2-P ouabain] and inhibit ATP hydrolysis and ion transport (Fig. lb, step 4). 

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