Calorimetric indication of the molten globule-like state of cytochrome c induced by n-alkyl sulfates at low concentrations

The molten globule state has been proposed as a major intermediate of protein folding. However it has proven difficult to obtain thermodynamic data characterizing this state. To explore an alternative approach for characterization of the molten globule state, n-alkyl sulfates induced formation of the molten globule state of horse cytochrome c at pH 2 was studied by isothermal titration calorimetry (ITC). Titration of the acid unfolded state of cytochrome c with sodium octyl sulfate, sodium dodecyl sulfate or sodium tetradecyl sulfate, generated an exothermic reaction for formation of the molten globule state. The effects of various n-alkyl sulfates on the acid unfolded state of cytochrome c demonstrated that the increased alkyl chain length enhanced the exothermic values of calorimetric enthalpy and induced a more compact molten globule states. The heat contents agreed well with the conformational transition measured by molar ellipticity at 222 nm ([θ]₂₂₂) and Stoke radius (Rs) values. These results emphasize that isothermal titration calorimetry provides a reasonable alternative method for characterization of the molten globule state.     

Solvation dynamics of a protein in the pre molten globule state

The nature of solvent molecules around proteins in native and different non-native states is crucial for understanding the protein folding problem. We have characterized two compact denatured states of glutaminyl-tRNA synthetase (GlnRS) under equilibrium conditions in the presence of a naturally occurring osmolyte, l-glutamate. The solvation dynamics of the compact denatured states and the fully unfolded state has been studied using a covalently attached probe, acrylodan, near the active site. The solvation dynamics progressively becomes faster as the protein goes from the native to the molten globule to the pre molten globule to the fully unfolded state. Anisotropy decay measurements suggest that the pre-molten-globule intermediate is more flexible than the molten globule although the secondary structure is largely similar. Dynamic light scattering studies reveal that both the compact denatured states are aggregated under the measurement conditions. The implications of solvation dynamics in aggregated compact denatured states have been discussed.     

Examination of intermediates in globular protein unfolding by the tritium labeling method

Unfolding of polypeptide chain of ribonuclease A in urea and guanidinium chloride (GuCl) solutions under equilibrium conditions involves formation of intermediates whose properties (compactness and preservation of the most of the native hydrophobic core, secondary structures, and native-like folding of the polypeptide chain) correspond to the basic characteristics of the “molten globule” state. Intermediates are “damp” molten globules (with water molecules inside the globule). The examinations performed revealed pronounced distinctions in the properties of the intermediates, above all, in their compactness degrees.     

New scenarios of protein folding can occur on the ribosome

Identifying and understanding the differences between protein folding in bulk solution and in the cell is a crucial challenge facing biology. Using Langevin dynamics, we have simulated intact ribosomes containing five different nascent chains arrested at different stages of their synthesis such that each nascent chain can fold and unfold at or near the exit tunnel vestibule. We find that the native state is destabilized close to the ribosome surface due to an increase in unfolded state entropy and a decrease in native state entropy; the former arises because the unfolded ensemble tends to behave as an expanded random coil near the ribosome and a semicompact globule in bulk solution. In addition, the unfolded ensemble of the nascent chain adopts a highly anisotropic shape near the ribosome surface and the cooperativity of the folding-unfolding transition is decreased due to the appearance of partially folded structures that are not populated in bulk solution. The results show, in light of these effects, that with increasing nascent chain length folding rates increase in a linear manner and unfolding rates decrease, with larger and topologically more complex folds being the most highly perturbed by the ribosome. Analysis of folding trajectories, initiated by temperature quench, reveals the transition state ensemble is driven toward compaction and greater native-like structure by interactions with the ribosome surface and exit vestibule. Furthermore, the diversity of folding pathways decreases and the probability increases of initiating folding via the N-terminus on the ribosome. We show that all of these findings are equally applicable to the situation in which protein folding occurs during continuous (non-arrested) translation provided that the time scales of folding and unfolding are much faster than the time scale of monomer addition to the growing nascent chain, which results in a quasi-equilibrium process. These substantial ribosome-induced perturbations to almost all aspects of protein folding indicate that folding scenarios that are distinct from those of bulk solution can occur on the ribosome.     

高分子研究中的一个知识问题——柔性链“从线团到小球”的构象变化

一条大分子链由许多小分子通过共价键连接而成.正是这一"连接"导致了大分子一些独特的物理性质及相关问题.本文希望阐明的就是这样一个小分子物理中没有的知识问题:小分子在溶剂中仅有溶或不溶2个状态;而自60年代起,理论学家们就预言一条柔性大分子链在溶解的状态下,其构象随着溶剂性质变差可以从无规线团蜷缩成一个单链小球.为了证明这一构象变化,实验学家们从70年代末起进行了大量的研究,直至90年代初期仍未观察到稳定的单链蜷缩小球.实验上这一长期悬而未解的问题困惑着众多研究者.甚至有理论学家在1993年报道,当今的样品制备和实验手段无法观察到一个热力学稳定的单链蜷缩小球.中国钱人元先生和一些其他研究者自80年代末期也开始关注与单链有关的问题.我们实验室从1993年开始另辟蹊径,通过制备和采用窄分布的热敏性水溶性高分子超长链,终于在1995年利用激光光散射首次观察到理论上预测的"线团到小球"的构象变化.随后,又揭示了变化过程中存在着一个全新的"融化球"构象以及在单链蜷缩小球中并无理论上预计的额外链互穿和打结.从得到的稳定单链蜷缩小球出发,我们又首次在实验上研究了"小球到线团"的过程,意外地观察到其在准理想状态附近滞后于"线团到小球"的构象变化,并证明该滞后可归于链蜷缩过程中形成的额外链内氢键.最后,借用红外纳秒脉冲激光加热的方法研究了"线团到小球"的蜷缩动力学,并发现其包含了在单个高分子链上"成核"和"粗化"先后2个过程.其中,"成核"过程与链长无关.经过近20年的努力,我们终于基本解决了这一近代高分子物理研究中与知识有关的重要问题,揭示了与其相关的一些大分子特有的物理性质.     

激光光散射研究聚(N-异丙基丙烯酰胺)单链及其智能凝胶微球在水中的相变(下)

（接上期）２聚（Ｎ－异丙基丙烯酰胺）微凝胶在水中的体积相变２．１理论部分凝胶体积相变热力学：聚合物凝胶的溶胀和蜷缩可以用膨胀因子α＝（Ｖ／Ｖ０）１／３＝（ΦＴ／ΦΘ）１／３来表征，其中ΦΘ的ΦＴ分别是温度Θ和Ｔ下凝胶网络的体积分数。在平均场理论中，中...     

Coil-to-globule transition by dissipative particle dynamics simulation

The dynamics of a collapsing polymer under a temperature quench in dilute solution is investigated by dissipative particles dynamics. Hydrodynamic interactions and many-body interaction are preserved naturally by incorporating explicit solvent particles in this approach. Our simulation suggests a four-stage collapse pathway: localized clusters formation, cluster coarsening in situ, coarsening involving global backbone conformation change into a crumpled globule, and compaction of the globule. For all the quench depths and chain lengths used in our study, collapse proceeds without the chain getting trapped in a metastable "sausage" configuration, as reported in some earlier studies. We obtain the time scales for each of the first three stages, as well as its scaling with the quench depths ξ and chain lengths N. The total collapse time scales as τ(c) ～ ξ(-0.46 ± 0.04)N(0.98 ± 0.09), with the quench depth and degree of polymerization.     

Temperature effects on radiation induced phenomena in polytetrafluoroetylene (PTFE)-Change of G-value

Temperature dependencies on the radiation induced phenomena and G-value of polytetrafluoroethylene (PTFE) have been studied in a temperature range 77–653 K. It is well known that main chain scission occurs very effectively below the melting temperature of PTFE (600 K). We have found in our experiments that G-value of chain scission increases significantly with increasing irradiation temperature, until 600 K. In addition to that, we have realized that crosslinking occurs by irradiation in the molten state at 613 K (Tabata, 1992; Oshima et al., 1995; Tabata et al., 1996). In the molten state, G-value of crosslinking was found to be 0.35 (number of crosslinking/100 eV absorption), as a lower limit, and the apparent G-value of chain scission is drastically reduced. Above 633 K, radiation induced crosslinking mainly occurs, however parallel thermal depolymerization or decomposition takes place to some extent.     

Site-specific hydration dynamics in the nonpolar core of a molten globule by dynamic nuclear polarization of water

Water-protein interactions play a direct role in protein folding. The chain collapse that accompanies protein folding involves extrusion of water from the nonpolar core. For many proteins, including apomyoglobin (apoMb), hydrophobic interactions drive an initial collapse to an intermediate state before folding to the final structure. However, the debate continues as to whether the core of the collapsed intermediate state is hydrated and, if so, what the dynamic nature of this water is. A key challenge is that protein hydration dynamics is significantly heterogeneous, yet suitable experimental techniques for measuring hydration dynamics with site-specificity are lacking. Here, we introduce Overhauser dynamic nuclear polarization at 0.35 T via site-specific nitroxide spin labels as a unique tool to probe internal and surface protein hydration dynamics with site-specific resolution in the molten globular, native, and unfolded protein states. The (1)H NMR signal enhancement of water carries information about the local dynamics of the solvent within ～10 ? of a spin label. EPR is used synergistically to gain insights on local polarity and mobility of the spin-labeled protein. Several buried and solvent-exposed sites of apoMb are examined, each bearing a covalently bound nitroxide spin label. We find that the nonpoloar core of the apoMb molten globule is hydrated with water bearing significant translational dynamics, only 4-6-fold slower than that of bulk water. The hydration dynamics of the native state is heterogeneous, while the acid-unfolded state bears fast-diffusing hydration water. This study provides a high-resolution glimpse at the folding-dependent nature of protein hydration dynamics.     

Probing the effect of temperature on the backbone dynamics of the human alpha-lactalbumin molten globule

Molten globules are compact, partially folded proteins postulated to be general intermediates in protein folding. Human alpha-lactalbumin (alpha-LA) is a two-domain Ca(2+)-binding protein that partially unfolds at low pH to form a molten globule. NMR spectra of molten globules are characterized by broadened resonances due to conformational fluctuations on microsecond to millisecond time scales. These species are often studied at high temperature where NMR resonances are observed to sharpen. The effect of higher temperatures on fast time-scale backbone dynamics of molten globules has not been investigated previously. Here, 1D (15)N direct-detection and 2D indirect-detection (1)H-(15)N heteronuclear NOE experiments have been used to probe fast time-scale dynamics at low and high temperatures for three disulfide-bond variants of human alpha-LA that form molten globules. Disulfide bonds are found to have a significant effect on backbone dynamics within the beta-domain of the molten globule; within the alpha-domain, dynamics are not significantly influenced by these bonds. At 20 degrees C, backbone mobility is significantly decreased in both domains of the molten globule compared to the mobility at 40-50 degrees C. Heteronuclear NOE values determined at 20 degrees C for the alpha-domain are closely similar to those observed for native alpha-LA, indicating that the alpha-LA molten globule has even more native-like character than suggested by studies conducted at higher temperature. Our results highlight the importance of considering the temperature dependence of the molten globule ensemble when making comparisons between experimental data obtained under different conditions.     

Thermodynamic analysis of partially folded states of myoglobin in presence of 2,2,2-trifluoroethanol

The thermal denaturation of myoglobin was studied in the presence of 2,2,2-trifluoroethanol (TFE) at various pH values using differential scanning calorimetry and UV–visible spectroscopy. The most obvious effect of TFE was lowering the transition temperature up to 1.5 mol · kg⁻¹, beyond which no thermal transitions were observed. The protein conformation was analysed by fluorescence and circular dichroism measurements. Quantitative binding of ANS to the TFE induced molten globule state of myoglobin was studied by using isothermal titration calorimetry. The results enable quantitative estimation of the binding strength of ANS with the molten globule state of myoglobin along with the enthalpic and entropic contributions to the binding process. The results suggest occurrence of common structural features of the molten globule states of proteins offering two types of binding sites to ANS molecules which are a widely used fluorescence probe to characterise partially folded states of proteins.     

Conformational properties of rigid-chain amphiphilic macromolecules: The phase diagram

The coil-globule transition in rigid-chain amphiphilic macromolecules was studied by means of computer simulation, and the phase diagrams for such molecules in the solvent quality-persistence length coordinates were constructed. It was shown that the type of phase diagram depends to a substantial extent on the degree of polymerization of a macromolecule. Relatively short amphiphilic macromolecules in the poor-solvent region always form a spherical globule, with the transition to this globule involving one or two intermediate conformations. These are the disk globule if the Kuhn segment is relatively large and the string of spherical micelles or the disk globule in the case of relative flexible chains. The phase diagram of a long rodlike amphiphilic chain turned out to be even more complex. Namely, three characteristic regions were distinguished in the region of a poor solvent, depending on the chain rigidity: the region of a cylindrical globule without certain order in the main chain, the region of the cylindrical globule with blobs having the collagen ordering of the chain, and the region of coexistence of collagen-like and toroidal globules. In the intermediate transitional region, not only conformations of strings of spherical micelle beads but also the necklace conformations in which the polymer chain in each bead has collagen ordering can occur in this case.     

Folding of ubiquitin: a simple model describes the strange kinetics

The ubiquitin mutant UbG folding experiments of Sabelko et al., in which "strange kinetics" were observed, are interpreted in terms of a simple kinetic model. A minimal set of states consisting of a semicompact globule, two off-pathway traps, and the native state are included; the fully unfolded state is not considered because folding to the semicompact globule is fast. Both the low- and the high-temperature experiments of Sabelko et al. are fitted by a system of kinetic equations determining the transitions between these states. It is possible that cold- and heat-denaturated states of UbG are the basis of the off-pathway traps. The fits of the kinetic model to the experimental results provides an estimate of the rate constants for the various reaction channels and show how their contributions vary with temperature. Introduction of an on-pathway intermediate instead of one of the off-pathway traps does not lead to agreement with the experiments.     

Nature of the cytochrome c molten globule

We have employed fluorescence energy transfer (FET) kinetics to probe unfolded and molten globule states of five dansyl (Dns) variants of Saccharomyces cerevisiae iso-1 cytochrome c. The covalently bound Fe(III) heme group quenches Dns fluorescence by energy transfer; measurements of FET kinetics yielded distributions of D-A distances (P(r)) for these states. The P(r) distributions and corresponding mean force potentials (U(r)) show that the cytochrome c molten globule is a highly structured state with a substantial number of native interactions. Wide P(r) distributions directly reflect the dynamic nature and conformational diversity of this molten globule. P(r) distributions for the "burst-phase" refolding intermediate suggest that the equilibrium cytochrome c molten globule is not a suitable model for early intermediates formed during protein refolding.     

高分子熔体结晶的两维计算机模拟

高分子熔体结晶的两维计算机模拟胡文兵，于同隐，卜海山（复旦大学高分子科学系，复旦大学材料科学系，上海，２００４３３）关键词计算机模拟，有序相变，高分子１９５６年Ｆｌｏｒｙ［１］从平均场近似的格子模型证明：高分子链的非柔顺性会导致长链的完全有序排列．此...     

Spectroscopic study on acid-induced unfolding and refolding of apo-neuroglobin

pH-induced unfolding and refolding of apo-neuroglobin (apo-Ngb) were investigated by UV, fluorescence, circular dichroism (CD) spectra and light scattering measurements. Results revealed that apo-Ngb became partially unfolded at around pH 5.0, with evidences from a red shift in the fluorescence spectra, a decrease in the far-UV CD and a sharp peak in the light scattering intensity. Further lowering of the pH reversed these effects, suggesting that apo-Ngb folds back to a compact state. At pH 2.0, the apo-Ngb forms a folding intermediate known as molten globule (MG), which is possessed of native-like secondary structure and almost complete loss of tertiary structure. Based on these results, the acid-induced denaturation pathway of apo-Ngb can be illustrated from the native state (N), via a partially unfolded state (U_A) to the molten globule state (MG).     

2,2,2-trifluoroethanol-induced molten globule state of concanavalin a and energetics of 8-anilinonaphthalene sulfonate binding: calorimetric and spectroscopic investigation

The interaction of 2,2,2-trifluoroethanol (TFE) with concanavalin A has been investigated by using a combination of differential scanning calorimetry, isothermal titration calorimetry (ITC), circular dichroism (CD), and fluorescence spectroscopy at pH 2.5 and 5.2. All of the calorimetric transitions at both the pH values were found to be irreversible. In the presence of 4 mol kg(-1) TFE at pH 2.5, concanavalin A is observed to be in a partially folded state with significant loss of native tertiary structure. The loss of specific side chain interactions in the transition from native to the TFE-induced partially folded state is demonstrated by the loss of cooperative thermal transition and reduction of the CD bands in the aromatic region. Acrylamide quenching, 8-anilinonaphthalene sulfonate (ANS) binding, and energy transfer also suggest that in the presence of 4 mol kg(-1) TFE at pH 2.5 concanavalin A is in a molten globule state. ITC has been used for the first time to characterize the energetics of ANS binding to the molten globule state. ITC results indicate that the binding of ANS to the molten globule state and acid-induced state at pH 2.5 displays heterogeneity with two classes of non-interacting binding sites. The results provide insights into the role of hydrophobic and electrostatic interactions in the binding of ANS to concanavalin A. The results also demonstrate that ITC can be used to characterize the partially folded states of the protein both qualitatively and quantitatively.     

Symmetry control of radiative decay in linear polyenes: low barriers for isomerization in the S1 state of hexadecaheptaene

The room temperature absorption and emission spectra of the 4-cis and all-trans isomers of 2,4,6,8,10,12,14-hexadecaheptaene are almost identical, exhibiting the characteristic dual emissions S1-->S0 (21Ag- --> 11Ag-) and S2-->S0 (11Bu+ --> 11Ag-) noted in previous studies of intermediate length polyenes and carotenoids. The ratio of the S1-->S0 and S2-->S0 emission yields for the cis isomer increases by a factor of approximately 15 upon cooling to 77 K in n-pentadecane. In contrast, for the trans isomer this ratio shows a 2-fold decrease with decreasing temperature. These results suggest a low barrier for conversion between the 4-cis and all-trans isomers in the S1 state. At 77 K, the cis isomer cannot convert to the more stable all-trans isomer in the 21Ag- state, resulting in the striking increase in its S1-->S0 fluorescence. These experiments imply that the S1 states of longer polyenes have local energy minima, corresponding to a range of conformations and isomers, separated by relatively low (2-4 kcal) barriers. Steady state and time-resolved optical measurements on the S1 states in solution thus may sample a distribution of conformers and geometric isomers, even for samples represented by a single, dominant ground state structure. Complex S1 potential energy surfaces may help explain the complicated S2-->S1 relaxation kinetics of many carotenoids. The finding that fluorescence from linear polyenes is so strongly dependent on molecular symmetry requires a reevaluation of the literature on the radiative properties of all-trans polyenes and carotenoids.