RESUMO
Preferential solvation is a fundamental parameter for the interpretation of solubility and solute structural stability. The molecular basis for solute-solvent interactions can be obtained through distribution functions, and the thermodynamic connection to experimental data depends on the computation of distribution integrals, specifically Kirkwood-Buff integrals for the determination of preferential interactions. Standard radial distribution functions, however, are not convenient for the study of the solvation of complex, nonspherical solutes, as proteins. Here we show that minimum-distance distribution functions can be used to compute KB integrals while at the same time providing an insightful view of solute-solvent interactions at the molecular level. We compute preferential solvation parameters for Ribonuclease T1 in aqueous solutions of urea and trimethylamine N-oxide (TMAO) and show that, while macroscopic solvation shows that urea is preferentially bound to the protein surface and TMAO is preferentially excluded, both display specific density augmentations at the protein surface in dilute solutions. Therefore, direct protein-osmolyte interactions can play a role in the stability and activity of the protein even for preferentially hydrated systems. The generality of the distribution function and its natural connection to thermodynamic data suggest that it will be useful in general for the study of solvation in mixtures of structurally complex solutes and solvents.
Assuntos
Ribonuclease T1/química , Solventes/química , Metilaminas/química , Simulação de Dinâmica Molecular , Ribonuclease T1/metabolismo , Termodinâmica , Ureia/químicaRESUMO
Este trabalho objetivou investigar a dependência entre o equilíbrio de desenovelamento da invertase por uréia, segundo um mecanismo de equilíbrio entre dois estados, com algumas propriedades termodinâmicas do solvente. Os valores das propriedades termodinâmicas do solvente foram calculados com aplicação da teoria de McMillian-Mayer. O equilíbrio de desenovelamento da invertase foi acompanhado por titulação espectrofotométrica em 280nm com uma solução de uréia a 8 mol.L-¹. O bom ajuste a um modelo de primeira ordem apresentado pelos dados de equilíbrio da invertase, bem como da RNase A e da RNase T1, é consistente com a idéia de que o alto conteúdo em carboidratos da invertase não afeta o mecanismo geral de desenovelamento. Entretanto, um aumento na concentração de uréia produziu uma diminuição na energia livre de desenovelamento (DeltaG°U ) para a intertase, e um aumento nos valores de DeltaG°U para Rnase A e Rnase T1. A invertase também exigiu maiores valores de atividade de água (Aw) do que a RNAse A e a RNAse T1 para ser desenovelada. O diferente comportamento da invertase em relação a aquelas enzimas pode ser relevante para fornecer informação adicional sobre os mecanismos detalhados do enovelamento e desenovelamento de proteínas.
Assuntos
Ribonuclease T1 , Ribonuclease Pancreático , Ribonucleases , Solventes , Termodinâmica , Ureia , ÁguaRESUMO
The X-ray crystal structure of a complex between ribonuclease T1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2. 0 A resolution. This ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both have a GpcU bound at the active site in the same manner. The protein-protein interface reveals an extended aromatic stack involving both guanines and three enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at the active site on enzyme molecule A and interacts with GpcU on molecule B in a neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine moieties of the three GpcU molecules in the asymmetric unit interacts directly with the protein. GpcU-active-site interactions involve extensive hydrogen bonding of the guanine moiety at the primary recognition site and of the guanosine 2'-hydroxyl group with His40 and Glu58. On the other hand, the phosphonate group is weakly bound only by a single hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate analogues and 3'-GMP, which hydrogen-bonded with three additional active-site residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate moiety is essentially the same as that recently observed for a novel structure of a RNase T1-3'-GMP complex obtained immediately after in situ hydrolysis of exo-(Sp)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents a nonproductive binding mode for GpU [Steyaert, J., and Engleborghs (1995) Eur. J. Biochem. 233, 140-144]. The results suggest that the active site of ribonuclease T1 is adapted for optimal tight binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in the transition state for catalytic transesterification, which is stabilized by adjacent binding of the leaving nucleoside (U) group.
Assuntos
Desoxiuridina/análogos & derivados , Fosfatos de Dinucleosídeos/química , Organofosfonatos/química , Ribonuclease T1/química , Aspergillus oryzae/enzimologia , Sítios de Ligação , Catálise , Cristalografia por Raios X , Desoxiuridina/química , Guanosina Monofosfato/química , Ligantes , Substâncias Macromoleculares , Modelos Moleculares , Estereoisomerismo , Especificidade por Substrato , TermodinâmicaRESUMO
We present a lattice Monte Carlo study to examine the effect of denaturants on the folding rates of simplified models of proteins. The two-dimensional model is made from a three-letter code mimicking the presence of hydrophobic, hydrophilic, and cysteine residues. We show that the rate of folding is maximum when the effective hydrophobic interaction epsilon H is approximately equal to the free energy gain epsilon S upon forming disulfide bonds. In the range 1 < or = epsilon H/ epsilon S < or = 3, multiple paths that connect several intermediates to the native state lead to fast folding. It is shown that at a fixed temperature and epsilon S the folding rate increases as epsilon H decreases. An approximate model is used to show that epsilon H should decrease as a function of the concentration of denaturants such as urea or guanidine hydrochloride. Our simulation results, in conjunction with this model, are used to show that increasing the concentration of denaturants can lead to an increase in folding rates. This occurs because denaturants can destabilize the intermediates without significantly altering the energy of the native conformation. Our findings are compared with experiments on the effects of denaturants on the refolding of bovine pancreatic trypsin inhibitor and ribonuclease T1. We also argue that the phenomenon of denaturant-enhanced folding of proteins should be general.