Alternating site mechanism

Gilbert SP, Moyer ML, Johnson KA. Alternating site mechanism of the kinesin ATPase. Biochemistry 1998 37 792-799. 

The soluble, extramembrane segment of the chloroplast ATP synthase, termed CFj, will hydrolyse ATP rapidly by a mechanism involving the cooperation of all three of its active sites - the alternating site mechanism. In the case of mitochondrial Fi, kinetic analysis suggests that, in the absence of cooperativity, this enzyme still possesses an intrinsic ATPase activity, but that in this mode each subunit turns over independendy - unisite catalysis [1]. We have confirmed that CF, can also operate in a similar manner [2],... 

Forms of BR and polyisobutylene. The properties of butyl rubber and polyisobutylene depend on their moleeular weight, degree of unsaturation, nature of the stabilizer incorporated during manufacture and, in some cases, chemical modification. It is common to produce halogenated forms of butyl rubber to increase polarity and to provide a reactive site for alternate cure mechanisms [6],... 

The initial step in the alternative hydrolysis mechanism is protonation of the ring 0i by Glu 35 (Scheme I). Cleavage of the endocyclic C1-O5 bond forms the acyclic oxocarbonium ion intermediate, which is stabilized by Asp 52. Attack by water, cleavage of the C1-O4 bond, and ring closure then lead to the observed products. Existing experimental data on lysozyme hydrolysis are consistent with Scheme I (see references in Post and Karplus ( )). Moreover, distortion of the ring in site D is not required and the antiperiplanar orientation of an exocyclic O4 lone pair orbital relative to the cleaved C1-O5 bond found in the simulation (see section on "Enhancement of a Substrate Conformation Optimum for Catalysis") is in accord with stereoelectronic requirements (1 ). ... 

These are standard reactions, and it does not matter which you do first. Resist the urge to do both at the same time it s unlikely to occur, and will certainly complicate your structures and mechanisms. Note that we have to include a number of protonations to make the mechanisms work. This is quite legitimate, and although the question has not specified any conditions, you can assume there will be a source of protons. In any case, you will observe that protons are first released to solvent, then transferred back to an alternative site in the molecule. 

Adsorption to the surfaces of ettringite and monosulphate is an alternative immobilization mechanism that has been examined for SeO , ScO and of AsO (Myneni et al. 1997 Baur 2002 Baur Johnson 2002a). The studies estimated a maximum surface site concentration of approximately 0.03-0.1 mol/kg... 

An alternative polymerization mechanism and polymer architecture has been proposed by Kirchhoff [1, 2, 3], Tan and Arnold [77], By this mechanism, polybenzocyclobutenes which do not contain reactive sites of unsaturation are proposed to polymerize by the 1,4 addition of the o-quinodimethane intermediates to give a substantially linear poly(o-xylylene) structure. Since the monomers all contain at least two benzocyclobutene units the net result of this reaction will to a first approximation be a ladder type polymer as shown in Fig. 17. The formation of a true ladder polymer however would require that all... 

Three types of elastomeric polypropylene are known (1) a large molecular weight atactic polymer [125], (2) polymers with alternating isotactic and atactic blocks [108,109,126-129], and (3) polymers formed by the dual-site mechanism [110]. The structure of the obtained elastomeric polypropylene was elucidated by comparison of the 13C-NMR spectra with those of an atactic oily polymer and isotactic polypropylene prepared by the zirconium complex 4. On the basis of the NMR data, for all the samples the statistical lengths of the isotactic blocks between two neighboring epimerization stereodefects were calculated [41]. It was found that for the isotactic polymer 90%), the... 

Senior and colleagues have introduced a reporter tryptophan in the catalytic sites of Escherichia coli Fi (EFi) and directly measured the site occupancy. They have shown that the ATP hydrolysis activity parallels the occupancy of the third site, implicating a tri-site mechanism where the site occupancy alternates between two and three, being three during the rate-limiting step of the catalysis [31,32], Studies on TFi basically corroborated the results [33,34],... 

Kashida 1990] and proton disorder could be an alternative decoherence mechanism. Crystal structures determined at various temperatures show that above 150 K protons are distributed over two sites located at 0.3 A off-center of the hydrogen bond (see below Sec. 3). The occupation ratio for the two sites increases from 4 96 at 200 K to 18 82 at 300 K. 

A structurally similar active site to that of carboxypeptidase A is found for the endopeptidase thermolysin.77 While several crystallographic and biochemical studies favor a zinc hydroxide mechanism for thermolysin (involving Glu-143 as a general base),80 in an alternative proposed mechanism for this enzyme, the zinc center is proposed to activate the substrate for nucleophilic attack by a non-coordinated water molecule (Scheme 14).81,82... 

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