Protein relaxation

Cirrhotic cardiomyopathy This term is defined as a left ventricular functional disorder due to stress (e. g. hyperdynamic circulation) or as pharmacological stimulation. But also the possibility of (toxically induced ) subclin-ical myocardial damage is discussed, especially because elevated troponin 1 serum values are detectable in every third patient. (81, 142, 187) (Troponin is connected with propomyosin in the actin filaments at regular intervals and, as a relaxing protein , has an important function in muscle metabolism, also in the heart). 

Continuum electrostatic models [72,108-113] are presently most developed and commonly nsed for the evaluation of the solvation energies in proteins however, they carry a nnmber of limitations and uncertainties, which cannot be avoided unless the microscopic interactions of the quantum subsystem and the protein are taken into account [114], For example, it is not clear which dielectric constant of the polarizable water cavities one should use in such calculations even the usually assumed dielectric constant of a dry protein (typically assumed as 4 [99,115,116]) is not that well defined—many studies indicate that the effective dielectric of the protein is much higher [114,117-119]— primarily due to internal water [120], and partially due to protein (nonlinear) charge relaxation. Proteins are also inhomogeneous media. It is understood that only microscopic simulations should eventually provide a correct picture and remove the inherent uncertainty of phenomenological approach [71,114,115,121-132]. Despite the drawbacks, the continuum models provide most computationally efficient approach for the treatment of the protein electrostatics, which make possible large-scale investigation of the enzyme properties, such as CcO. 

Relaxation protein a type I eukaryotic topoiso-merase (see Topoisomerases) isolated from the nuclei of LA9 mouse and HeLa cells, and characterized by its ability to remove superhelical firms from closed, circular DNA. [H-P. Vosberg etal. Eur. J.Biochem. 55 (1975) 79-93]... 

The following enzymes described in the literature are now known to be type I T E. coll w-protein (identical with Eco DNA T., . coU swivelase, and E. cell type IT.), untwisting enzymes, nicking-closing enzymes, Relaxation protein (see), DNA-Relaxing enzyme (see). 

The cross-correlation effects between the DD and CSA interactions also influence the transverse relaxation and lead to the phenomenon known as differential line broadening in a doublet [40], cf Figure Bl.13.8. There is a recent experiment, designed for protein studies, that I wish to mention at tire end of this section. It has been proposed by Pervushin etal [4T], is called TROSY (transverse relaxation optimized spectroscopy) and... 

Dayie K T, Wagner G and Lefeevre J F 1996 Theory and practice of nuclear spin relaxation in proteins Anna. Rev. Phys. Chem. 47 243-82... 

Tjandra N, Szabo A and Bax A 1996 Protein backbone dynamics and N-15 chemical shift anisotropy from quantitative measurement of relaxation interference effected. Am. Chem. Soc. 118 6986-91... 

Averbukh I Sh, Blumenfeld L A, Kovarsky V A and Perelman N F 1986 A model of the mechanism of enzyme action in terms of protein conformational relaxation Blochim. Blophys. Acta. 873 290-6... 

Figure C3.1.7. Time-resolved optical absorjDtion data for the Soret band of photo lysed haemoglobin-CO showing six first-order (or pseudo-first-order) relaxation phases, I-VI, on a logaritlimic time scale extending from nanoseconds to seconds. Relaxations correspond to geminate and diffusive CO rebinding and to intramolecular relaxations of tertiary and quaternary protein stmcture. (From Goldbeck R A, Paquette S J, Bjorling S C and Kliger D S 1996 Biochemistry 35 8628-39.)...

The simulations also revealed that flapping motions of one of the loops of the avidin monomer play a crucial role in the mechanism of the unbinding of biotin. The fluctuation time for this loop as well as the relaxation time for many of the processes in proteins can be on the order of microseconds and longer (Eaton et al., 1997). The loop has enough time to fluctuate into an open state on experimental time scales (1 ms), but the fluctuation time is too long for this event to take place on the nanosecond time scale of simulations. To facilitate the exit of biotin from its binding pocket, the conformation of this loop was altered (Izrailev et al., 1997) using the interactive molecular dynamics features of MDScope (Nelson et al., 1995 Nelson et al., 1996 Humphrey et al., 1996). 

Molecular dynamics simulations of proteins often begin with a known structure (such as an X-ray diffraction structure) that you want to maintain during equilibration. Since the solvent may contain high energy hot spots, equilibration of the protein and solvent at the same time can change the protein conformation. To avoid this, select only the water molecules and run a molecular dynamics equilibration. This relaxes the water while fixing the protein structure. Then deselect the water and equilibrate the whole system. 

In addition, vinpocetine selectively inhibits a specific calcium, calmodulin-dependent cycHc nucleotide phosphodiesterase (PDF) isozyme (16). As a result of this inhibition, cycHc guanosine 5 -monophosphate (GMP) levels increase. Relaxation of smooth muscle seems to be dependent on the activation of cychc GMP-dependent protein kinase (17), thus this property may account for the vasodilator activity of vinpocetine. A review of the pharmacology of vinpocetine is available (18). 

Contraction of muscle follows an increase of Ca " in the muscle cell as a result of nerve stimulation. This initiates processes which cause the proteins myosin and actin to be drawn together making the cell shorter and thicker. The return of the Ca " to its storage site, the sarcoplasmic reticulum, by an active pump mechanism allows the contracted muscle to relax (27). Calcium ion, also a factor in the release of acetylcholine on stimulation of nerve cells, influences the permeabiUty of cell membranes activates enzymes, such as adenosine triphosphatase (ATPase), Hpase, and some proteolytic enzymes and facihtates intestinal absorption of vitamin B 2 [68-19-9] (28). 

In the presence of calcium, the primary contractile protein, myosin, is phosphorylated by the myosin light-chain kinase initiating the subsequent actin-activation of the myosin adenosine triphosphate activity and resulting in muscle contraction. Removal of calcium inactivates the kinase and allows the myosin light chain to dephosphorylate myosin which results in muscle relaxation. Therefore the general biochemical mechanism for the muscle contractile process is dependent on the avaUabUity of a sufficient intraceUular calcium concentration. 

Q Zheng, R Rosenfeld, S Vajda, C DeLisi. Determining protein loop conformation using scahng-relaxation techniques. Protein Sci 2 1242-1248, 1993. 

Parvalbumin is a muscle protein with a single polypeptide chain of 109 amino acids. Its function is uncertain, but calcium binding to this protein probably plays a role in muscle relaxation. The helix-loop-helix motif appears three times in this structure, in two of the cases there is a calcium-binding site. Figure 2.13 shows this motif which is called an EF hand because the fifth and sixth helices from the amino terminus in the structure of parvalbumin, which were labeled E and F, are the parts of the structure that were originally used to illustrate calcium binding by this motif. Despite this trivial origin, the name has remained in the literature. 

In the native protein these less stable ds-proline peptides are stabilized by the tertiary structure but in the unfolded state these constraints are relaxed and there is an equilibrium between ds- and trans-isomers at each peptide bond. When the protein is refolded a substantial fraction of the molecules have one or more proline-peptide bonds in the incorrect form and the greater the number of proline residues the greater the fraction of such molecules. Cis-trans isomerization of proline peptides is intrinsically a slow process and in vitro it is frequently the rate-limiting step in folding for those molecules that have been trapped in a folding intermediate with the wrong isomer. 

The theory predicts that such proteins are built up of several subunits which are symmetrically arranged and that the two states differ by the arrangements of the subunits and the number of bonds between them. In one state the subunits are constrained by strong bonds that would resist the structural changes needed for substrate binding, and this state would consequently bind substrates weakly they called it the tense or T state. In the other state, called the R state, these constraints are relaxed. 

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. 

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