Folding rate

The key question we want to answer is what are the intrinsic sequence dependent factors tliat not only detennine tire folding rates but also tire stability of tire native state It turns out tliat many of tire global aspects of tire folding kinetics of proteins can be understood in tenns of tire equilibrium transition temperatures. In particular, we will show tliat tire key factor tliat governs tire foldability of sequences is tire single parameter... 

Using lattice models we have also established tliat folding rates correlate well witli Z = (E - / 5, where E- is... 

D. K. Klimov and D. Thirumalai. Viscosity dependence of the folding rates of proteins. Phys. Rev. Lett., 79 317-320, 1997. 

The relative importance of the potential catalytic mechanisms depends on pH, which also determines the concentration of the other participating species such as water, hydronium ion, and hydroxide ion. At low pH, the general acid catalysis mechanism dominates, and comparison with analogous systems in which the intramolecular proton transfer is not available suggests that the intramolecular catalysis results in a 25- to 100-fold rate enhancement At neutral pH, the intramolecular general base catalysis mechanism begins to operate. It is estimated that the catalytic effect for this mechanism is a factor of about 10. Although the nucleophilic catalysis mechanism was not observed in the parent compound, it occurred in certain substituted derivatives. 

Secondary steric effects of the same kind have been found in the reaction of methyl derivatives of 22 with aniline. A methyl group at position 6 has a 4-fold rate-diminishing effect (mainly inductive), but when positions 4 and 6 are both methylated the effect is 81-fold and is mainly of steric origin. 

The effect of salt (KN03) concentration is small, i.e. less than a two fold rate increase by increasing the salt concentration up to 0.2 M. 

Miller and Wolfenden, 2002). This latter ratio is the inverse of the rate enhancement achieved by the enzyme. In other words, the enzyme active site will have greater affinity for the transition state structure than for the ground state substrate structure, by an amount equivalent to the fold rate enhancement of the enzyme (rearranging, we can calculate KJX = Ksik Jk, )). Table 2.2 provides some examples of enzymatic rate enhancements and the calculated values of the dissociation constant for the /A binary complex (Wolfenden, 1999). 

Methylmalonyl-CoA mutase (MCM) catalyzes a radical-based transformation of methylmalonyl-CoA (MCA) to succinyl-CoA. The cofactor adenosylcobalamin (AdoCbl) serves as a radical reservoir that generates the S -deoxyadenosine radical (dAdo ) via homolysis of the Co—C5 bond [67], The mechanisms by which the enzyme stabilizes the homolysis products and achieve an observed 1012-fold rate acceleration are yet not fully understood. Co—C bond homolysis is directly kineti-cally coupled to the proceeding hydrogen atom transfer step and the products of the bond homolysis step have therefore not been experimentally characterized. 

In an effort to apply the cooperative principles of metalloenzyme reactivity, involving a combination of metal-ligand and hydrogen bonding, we have reported a ruthenium catalyst incorporating imidazolyl phosphine ligands that efficiently and selectively hydrates terminal alkynes (5). We subsequently found that application of pyridyl phosphines to the reaction resulted in a >10-fold rate enhancement and complete anti-Markovnikov selectivity, even in the... 

Singhal, N. Snow, C. D. Pande, V. S., Using path sampling to build better Markovian state models predicting the folding rate and mechanism of a tryptophan zipper beta hairpin, J. Chem. Phys. Jul 2004,121, 415—425. 

A 6- to 48-fold rate enhancement was observed for this reaction. The authors suggested that a nonthermal effect might account for this enhancement [56],... 

In Czamik s model compound 6 both cobalt(III) ions are presented in the same molecule [33]. Two (cyclen)Co(IH) units are covalently linked by a 1,4-dibutylbenzene spacer. By 6 the activated phosphodiester BNPP at pH 7.0 and 25 °C is hydrolyzed 3.2 times faster than by 2 equiv of (cyclen)Co(III) (7) under the same conditions. A more than 107-fold rate enhancement over the spontaneous hydrolysis of BNPP is observed. The reaction mechanism may be similar to that proposed for compound 2. 

Also, Chin s dihydroxy-bridged dicobalt(III) complex 10 provides one of the largest rate enhancements ever observed for phosphodiester hydrolysis [36]. Reaction with the activated phosphodiester methyl(p-nitrophenyl)phosphate (MNPP) yields 11. A crystal structure is available for the analogous dimethylphosphate complex in which the Co ions are 2.9 A apart. At pH 7 and 45 °C 11 releases p-nitrophenolate with k = 0.1 s 1 which corresponds to a nearly 10I2-fold rate enhancement over spontaneous hydrolysis of the substrate. The product of the reaction is a methylphosphate-bridged complex. Based on the pH rate profile and on... 

Even more efficient bimetallic cooperativity was achieved by the dinuclear complex 36 [53]. It was demonstrated to cleave 2, 3 -cAMP (298 K) and ApA (323 K) with high efficiency at pH 6, which results in 300-500-fold rate increase compared to the mononuclear complex Cu(II)-[9]aneN at pH 7.3. The pH-metric study showed two overlapped deprotonations of the metal-bound water molecules near pH 6. The observed bell-shaped pH-rate profiles indicate that the monohydroxy form is the active species. The proposed mechanism for both 2, 3 -cAMP and ApA hydrolysis consists of a double Lewis-acid activation of the substrates, while the metal-bound hydroxide acts as general base for activating the nucleophilic 2 -OH group in the case of ApA (36a). Based on the 1000-fold higher activity of the dinuclear complex toward 2, 3 -cAMP, the authors suggest nucleophilic catalysis of the Cu(II)-OH unit in 36b. The latter mechanism is comparable to those of protein phosphatase 1 and fructose 1,6-diphosphatase. 

These investigators also compared the folding rates of mercaptal-... 

The buried Cys-212 of human carbonic anhydrase B (3 pM) is virtually unreactive towards 2-chloromercuric-4-nitrophenol (60 pM) at pH 9.2, but upon the addition of only 40 pM CN , the half-life drops to 10 minutes which is an, at least, 75-fold rate enhancement. On first analysis, this would suggest that inhibitor binding to the enzyme has produced a conformational change or altered the — SH environment of the Cys—212. This is unexpected. How would you prove by kinetic experiments that the CN is binding to the mercury compound and not the enzyme and that this is changing the reactivity. The rate reaches a constant value at high [CN ]. 

There is strong evidence for a dissociative type of mechanism for base hydrolysis. There is an =10 -fold rate enhancement (steric acceleration) for base hydrolysis of Co(iso-BuNH2)5CP+ compared to Co(NH3)jCF (mainly residing in while the corresponding factor for aquation is only =<10, emphasizing the different degrees of dissociation D vs /j). There is, incidentally, a LFER for log Atqh vs log slope 1.0, for reactions of a series of Co(III) complexes. Finally, on the basis of a mechanism, the estimated pro-... 

The structure of the ribosomal protein L9 from B. stearothermophilus is shown in Fig. 3. The folding kinetics and thermodynamics of its C-terminal domain have been studied as a function of pH by NMR and CD spectroscopies. The ionization state of the two histidines (Hisl06 and His 134) was found to be essential for the global stability and the folding rate of the protein. ... 

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