Single molecule force spectroscopy reveals the context dependent folding pathway of the C-terminal fragment of Top7

Top7 is a de novo designed protein with atomic level accuracy and shows a folded structure not found in nature. Previous studies showed that the folding of Top7 is not cooperative and involves various folding intermediate states. In addition, various fragments of Top7 were found to fold on their own in isolation. These features displayed by Top7 are distinct from those of naturally occurring proteins of a similar size and suggest a rough folding energy landscape. However, it remains unknown if and how the intra-polypeptide chain interactions among the neighboring sequences of Top7 affect the folding of these Top7 fragments. Here we used single-molecule optical tweezers to investigate the folding–unfolding pathways of full length Top7 as well as its C-terminal fragment (CFr) in different sequence environments. Our results showed that the mechanical folding of Top7 involves an intermediate state that likely involves non-native interactions/structure. More importantly, we found that the folding of CFr is entirely dependent upon its sequence context in which it is located. When in isolation, CFr indeed folds into a cooperative structure showing near-equilibrium unfolding–folding transitions at ∼6.5 pN in OT experiments. However, CFr loses its autonomous cooperative folding ability and displays a folding pathway that is dependent on its interactions with its neighboring sequence/structure. This context-dependent folding dynamics and pathway of CFr are distinct from those of naturally occurring proteins and highlight the critical importance of intra-chain interactions in shaping the overall energy landscape and the folding pathway of Top7. These new insights may have important implications on the de novo design of proteins.

Optical tweezers experiments reveal that the folding of the C-terminal fragment of Top7 (cFr) is context-dependent. Depending on its neighboring sequence, cFr shows very different folding pathways and folding kinetics.      

Conformational Variability of Amyloid-β and the Morphological Diversity of Its Aggregates

Protein folding is the most fundamental and universal example of biomolecular self-organization and is characterized as an intramolecular process. In contrast, amyloidogenic proteins can interact with one another, leading to protein aggregation. The energy landscape of amyloid fibril formation is characterized by many minima for different competing low-energy structures and, therefore, is much more enigmatic than that of multiple folding pathways. Thus, to understand the entire energy landscape of protein aggregation, it is important to elucidate the full picture of conformational changes and polymorphisms of amyloidogenic proteins. This review provides an overview of the conformational diversity of amyloid-β (Aβ) characterized from experimental and theoretical approaches. Aβ exhibits a high degree of conformational variability upon transiently interacting with various binding molecules in an unstructured conformation in a solution, forming an α-helical intermediate conformation on the membrane and undergoing a structural transition to the β-conformation of amyloid fibrils. This review also outlines the structural polymorphism of Aβ amyloid fibrils depending on environmental factors. A comprehensive understanding of the energy landscape of amyloid formation considering various environmental factors will promote drug discovery and therapeutic strategies by controlling the fibril formation pathway and targeting the consequent morphology of aggregated structures.     

Asymmetric Modulation of Protein Order–Disorder Transitions by Phosphorylation and Partner Binding

As for many intrinsically disordered proteins, order–disorder transitions in the N‐terminal oligomerization domain of the multifunctional nucleolar protein nucleophosmin (Npm‐N) are central to its function, with phosphorylation and partner binding acting as regulatory switches. However, the mechanism of this transition and its regulation remain poorly understood. In this study, single‐molecule and ensemble experiments revealed pathways with alternative sequences of folding and assembly steps for Npm‐N. Pathways could be switched by altering the ionic strength. Phosphorylation resulted in pathway‐specific effects, and decoupled folding and assembly steps to facilitate disorder. Conversely, binding to a physiological partner locked Npm‐N in ordered pentamers and counteracted the effects of phosphorylation. The mechanistic plasticity found in the Npm‐N order–disorder transition enabled a complex interplay of phosphorylation and partner‐binding steps to modulate its folding landscape.     

Thermal crystallization studies on Ga−Te glasses

Semiconducting Ga_xTe_100?x (17≤x≤25) glasses have been prepared by melt quenching method and thermal crystallization studies carried out using differential scanning calorimetry. On heating, virgin Ga_xTe_100?x glasses exhibit one glass transition and two crystallization reactions. The first crystallization reaction corresponds to the precipitation of hexagonal Te and the second one to the crystallization of the matrix into zinc blende Ga₂Te₃ phase. If Ga_xTe_100?x glasses are quenched to ambient temperature fromT _crl and reheated, they exhibit the phenomenon of double glass transition.     

The kinetics of phase transitions in vitreous chalcogenide semiconductors As10.2Se89.8 and As9Se90Bi in early stage of physical ageing process

The kinetics of glass transition in selenide glasses As_10.2Se_89.8 and As₉Se₉₀Bi in early stage of physical ageing process has been investigated by parallel differential scanning calorimetry (DSC) and exoelectron emission (EEE). It has been found that the glass transition process occurring in investigated glasses is evidenced by peaks on EEE intensity and DSC curves. Admixture of bismuth causes a distinct lowering of the temperature of glass transitions process both in the surface layer and in the volume. The addition of Bi causes a decrease in the value of the activation energy for glass transition process in both the volume and in the surface layer, thus reducing the thermal stability of investigated glasses. Physical ageing in Se-rich chalcogenide glasses leads to a significant increase of endothermic peak area A, temperature of glass transition T _g and decrease of the activation energy value E. All these effects are strongly dependent on glass composition.     

Correlation between glass transition and crystallization phenomena in context of Meyer–Neldel rule

The physical origin of the glass transition and its possible connection with crystallization is still an unresolved problem of glass science. Recent publications demonstrate the strong evidence of intrinsic relation between glass transition and crystallization phenomena. Here, we study this problem by using Meyer–Neldel rule (MNR) as a tool. The observation of MNR in thermally activated non-isothermal crystallization was verified by us in past. The objective of the present work is to check the applicability of MNR for thermally activated non-isothermal glass transition and crystallization in some chalcogenide glasses. We found that like crystallization, the glass transition phenomenon also obeys the MNR.     

Space-time thermodynamics and subsystem observables in a kinetically constrained model of glassy materials

In a recent article [M. Merolle et al., Proc. Natl. Acad. Sci. U.S.A. 102, 10837 (2005)], it was argued that dynamic heterogeneity in d-dimensional glass formers is a manifestation of an order-disorder phenomenon in the d+1 dimensions of space time. By considering a dynamical analog of the free energy, evidence was found for phase coexistence between active and inactive regions of space time, and it was suggested that this phenomenon underlies the glass transition. Here we develop these ideas further by investigating in detail the one-dimensional Fredrickson-Andersen (FA) model, in which the active and inactive phases originate in the reducibility of the dynamics. We illustrate the phase coexistence by considering the distributions of mesoscopic space-time observables. We show how the analogy with phase coexistence can be strengthened by breaking microscopic reversibility in the FA model, leading to a nonequilibrium theory in the directed percolation universality class.     

Thermal stability and folding kinetics analysis of disordered protein,securin

Lacking a stable tertiary structure, intrinsically disordered proteins (IDPs) possess particular functions in cell regulation, signaling, and controlling pathways. The study of their unique structural features, thermal stabilities, and folding kinetics is intriguing. In this study, an identified IDP, securin, was used as a model protein. By using a quasi-static five-step (on-path) folding process, the function of securin was restored and analyzed by isothermal titration calorimetry. Fluorescence spectroscopy and particle size analysis indicated that securin possessed a compact hydrophobic core and particle size. The glass transition of securin was characterized using differential scanning microcalorimetry. Furthermore, the folding/unfolding rates (k_obs) of securin were undetectable, implying that the folding/unfolding rate is very fast and that the conformation of securin is sensitive to solvent environmental change. Therefore, securin may fold properly under specific physiological conditions. In summary, the thermal glass transition behavior and undetectable k_obs of folding/unfolding reactions may be two of the indices of IDP.     

Structural instability of metallic glasses under radio-frequency-ultrasonic perturbation and its correlation with glass-to-crystal transition of less-stable metallic glasses

It has been reported that the structural stability is significantly deteriorated under radio-frequency-ultrasonic perturbation at relatively low temperatures, e.g., near/below the glass transition temperature T(g), even for thermally stable metallic glasses. Here, we consider an underlying mechanism of the ultrasound-induced instability, i.e., crystallization, of a glass structure to grasp the nature of the glass-to-liquid transition of metallic glasses. Mechanical spectroscopy analysis indicates that the instability is caused by atomic motions resonant with the dynamic ultrasonic-strain field, i.e., atomic jumps associated with the beta relaxation that is usually observed for low frequencies of the order of 1 Hz at temperatures far below T(g). Such atomic motions at temperatures lower than the so-called kinetic freezing temperature T(g) originate from relatively weakly bonded (and/or low-density) regions in a nanoscale inhomogeneous microstructure of glass, which can be straightforwardly inferred from a partially crystallized microstructure obtained by annealing of a Pd-based metallic glass just below T(g) under ultrasonic perturbation. According to this nanoscale inhomogeneity concept, we can reasonably understand an intriguing characteristic feature of less-stable metallic glasses (fabricated only by rapid melt quenching) that the crystallization precedes the glass transition upon standard heating but the glass transition is observable at extremely high rates. Namely, in such less-stable metallic glasses, atomic motions are considerably active at some local regions even below the kinetic freezing temperature. Thus, the glass-to-crystal transition of less-stable metallic glasses is, in part, explained with the present nanoscale inhomogeneity concept.     

Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations

The study of the mechanism which is at the basis of the phenomenon of protein folding requires the knowledge of multiple folding trajectories under biological conditions. Using a biasing molecular-dynamics algorithm based on the physics of the ratchet-and-pawl system, we carry out all-atom, explicit solvent simulations of the sequence of folding events which proteins G, CI2, and ACBP undergo in evolving from the denatured to the folded state. Starting from highly disordered conformations, the algorithm allows the proteins to reach, at the price of a modest computational effort, nativelike conformations, within a root mean square deviation (RMSD) of approximately 1 A?. A scheme is developed to extract, from the myriad of events, information concerning the sequence of native contact formation and of their eventual correlation. Such an analysis indicates that all the studied proteins fold hierarchically, through pathways which, although not deterministic, are well-defined with respect to the order of contact formation. The algorithm also allows one to study unfolding, a process which looks, to a large extent, like the reverse of the major folding pathway. This is also true in situations in which many pathways contribute to the folding process, like in the case of protein G.     

Hiking down the energy landscape: progress toward the Kauzmann temperature via vapor deposition

Physical vapor deposition was employed to prepare amorphous samples of indomethacin and 1,3,5-(tris)naphthylbenzene. By depositing onto substrates held somewhat below the glass transition temperature and varying the deposition rate from 15 to 0.2 nm/s, glasses with low enthalpies and exceptional kinetic stability were prepared. Glasses with fictive temperatures that are as much as 40 K lower than those prepared by cooling the liquid can be made by vapor deposition. As compared to an ordinary glass, the most stable vapor-deposited samples moved about 40% toward the bottom of the potential energy landscape for amorphous materials. These results support the hypothesis that enhanced surface mobility allows stable glass formation by vapor deposition. A comparison of the enthalpy content of vapor-deposited glasses with aged glasses was used to evaluate the difference between bulk and surface dynamics for indomethacin; the dynamics in the top few nanometers of the glass are about 7 orders of magnitude faster than those in the bulk at Tg - 20 K.     

Dynamic light scattering in mixed alkali metaphosphate glass forming liquids

We report the first ever photon correlation spectroscopy performed on single alkali and mixed alkali metaphosphate glasses at refractory temperatures above the glass transition. We find not only a significant decrease in the glass transition temperature but also a decrease in fragility for the mixed alkali composition as compared with the single akali glasses. We argue that structural relaxation in these polymeric oxide glasses is largely controlled by the cross linking cations and that the changes in fragility that we observed are a reflection of changes in the cooperativity of structural relaxation wrought by the substantial decrease in the ion mobility that accompanies the mixing of alkali ions.     

Understanding the folding rates and folding nuclei of globular proteins

The first part of this paper contains an overview of protein structures, their spontaneous formation ("folding"), and the thermodynamic and kinetic aspects of this phenomenon, as revealed by in vitro experiments. It is stressed that universal features of folding are observed near the point of thermodynamic equilibrium between the native and denatured states of the protein. Here the "two-state" ("denatured state" <--> "native state") transition proceeds without accumulation of metastable intermediates, but includes only the unstable "transition state". This state, which is the most unstable in the folding pathway, and its structured core (a "nucleus") are distinguished by their essential influence on the folding/unfolding kinetics. In the second part of the paper, a theory of protein folding rates and related phenomena is presented. First, it is shown that the protein size determines the range of a protein's folding rates in the vicinity of the point of thermodynamic equilibrium between the native and denatured states of the protein. Then, we present methods for calculating folding and unfolding rates of globular proteins from their sizes, stabilities and either 3D structures or amino acid sequences. Finally, we show that the same theory outlines the location of the protein folding nucleus (i.e., the structured part of the transition state) in reasonable agreement with experimental data.     

Snapshotting the transient conformations and tracing the multiple pathways of single peptide folding using a solid-state nanopore

A fundamental question relating to protein folding/unfolding is the time evolution of the folding of a protein into its precisely defined native structure. The proper identification of transition conformations is essential for accurately describing the dynamic protein folding/unfolding pathways. Owing to the rapid transitions and sub-nm conformation differences involved, the acquisition of the transient conformations and dynamics of proteins is difficult due to limited instrumental resolution. Using the electrochemical confinement effect of a solid-state nanopore, we were able to snapshot the transient conformations and trace the multiple transition pathways of a single peptide inside a nanopore. By combining the results with a Markov chain model, this new single-molecule technique is applied to clarify the transition pathways of the β-hairpin peptide, which shows nonequilibrium fluctuations among several blockage current stages. This method enables the high-throughput investigation of transition pathways experimentally to access previously obscure peptide dynamics, which is significant for understanding the folding/unfolding mechanisms and misfolding of peptides or proteins.

A solid-state nanopore based method is described for resolving protein-folding-related problems via snapshotting the folding intermediates and characterizing the kinetics of a single peptide.     

高分子链的去拥挤转变及低温流动

简述了拥挤理论的基本原理,运用拥挤理论来说明高分子链间弱相互作用对高分子链所处的状态的影响,特别是对高分子玻璃化转变的影响.在实验中,采用固体核磁共振方法探测高分子的链间邻近度,并比较了不同链间邻近度的高分子样品在玻璃化转变温度以下的压力诱导流行行为,发现即使测试温度比高分子玻璃化转变温度低132℃,高分子链在压力下依...     

Structure–property relationships in multicomponent oxide glasses

Cations play a complex structural role in oxide glasses, as they occur in different kinds of environments, which allow them to exert a contrasted influence on physical and chemical properties of these glasses. The combination of structural information given by a wide range of spectroscopic methods and by radiation scattering, combined with numerical modelling, has given insight on the structural organisation around these cations. Among these characteristic properties are unusually low-coordination numbers, such as 5-fold coordination, and the presence of extended ordered domains, in which cation polyhedra are edge- or corner-sharing. This review presents evidence for a structural control of several physical and chemical properties in oxide multicomponent glasses. The use of zinc as a stabilising glass component arises from its network-forming position, which implies the presence of low-charge cations in its surrounding and as a consequence decreases the concentration of modifier components. The compositional dependence of glass coloration by transition elements has been investigated thoroughly through the example of nickel in silicate and borate glasses. The wide range of coloration observed may be explained by the existence of three kinds of environments, with nickel occurring in 4-, 5-, and 6- coordination. The relationships of these sites with the medium-range organisation of the glasses have been understood by a combined use of EXAFS spectroscopy and neutron scattering with isotopic substitution. The two other examples that are presented to illustrate structure–property relationships concern the physical solubility of gazes in glasses and the alteration processes of glasses used as analogues of nuclear waste matrices. In this last example, the use of structural probes as zirconium illustrates the influence of the alteration solution on the process of glass corrosion and further development of a gel at the glass–solution interface. A comparison with the evolution of the surrounding of iron shows that the two major processes, hydrolysis/condensation and dissolution/precipitation, depend on the element considered.     

The Non-Isothermal Devitrification of Glasses in the SrO·4GeO2−BaO·4GeO2 Composition Range

The effect of replacing SrO by BaO on the glass transition temperature and on devitrification behaviour in a series of glasses in the strontium tetragermanate — barium tetragermanate composition range has been studied by differential thermal analysis, X-ray diffraction and Fourier-transform infrared spectra. All glasses studied exhibit internal crystal nucleation. The progressive replacing of SrO by BaO causes the decrease of the glass transition temperature. Solid solutions between SrGe₄O₉ and BaGe₄O₉ were found to crystallize in glass containing both SrO and BaO. The effect of the specific surface of the glass samples on devitrification processes has been also pointed out.This revised version was published online in November 2005 with corrections to the Cover Date.     

Inherent structure analysis of protein folding

An analysis in terms of the inherent structures (IS, local minima) of the multidimensional potential energy landscape is applied to proteins. Detailed calculations are performed for the 46 bead BLN model, which folds into a four-stranded beta-barrel. Enhanced sampling has allowed determination of 239 199 IS states, believed to encompass nearly all the compact, low-energy states, and of well-averaged thermodynamic quantities at low temperature. The density of states shows distinct lobes for compact and extended states, and entropic barriers for the collapse and local ordering transitions. A two-dimensional scatterplot or density of states clearly shows the multifunnel structure of the energy landscape. The anharmonic vibrational free energy is found to play a crucial role in protein folding. The problem of determining the folding transition in a multifunnel system is discussed, and novel indicators of folding are introduced. A particularly clear picture is obtained through the occupation probabilities, pi, of individual low-lying IS, which become finite below the collapse temperature; it is suggested that poor foldability corresponds to a large "misfolding interval" where the excited state pi>0 exceeds that of the native state p0.     

The interplay of nonlinearity and architecture in equilibrium cytoskeletal mechanics

The interplay between cytoskeletal architecture and the nonlinearity of the interactions due to bucklable filaments plays a key role in modulating the cell's mechanical stability and affecting its structural rearrangements. We study a model of cytoskeletal structure treating it as an amorphous network of hard centers rigidly cross-linked by nonlinear elastic strings, neglecting the effects of motorization. Using simulations along with a self-consistent phonon method, we show that this minimal model exhibits diverse thermodynamically stable mechanical phases that depend on excluded volume, cross-link concentration, filament length, and stiffness. Within the framework set by the free energy functional formulation and making use of the random first order transition theory of structural glasses, we further estimate the characteristic densities for a kinetic glass transition to occur in this model system. Network connectivity strongly modulates the transition boundaries between various equilibrium phases, as well as the kinetic glass transition density.     

StepScan DSC

StepScan DSC technique was used for the study of the glass transition phenomenon. This method allows relatively good monitoring of reversing and non-reversing processes, and thus is very useful tool for glass transition studies of wide type of glass-forming materials, including inorganic glasses as well as organic polymers. In this work, experience with the StepScan DSC technique is summarized. Some interesting results of its application are presented, such as determination of glass transition temperature independent on thermal history of glass, discovered relationship between the slope of temperature dependence of C _p in T _g, and Angel’s index of fragility and estimation of viscosity glass transition temperature, T _g,η.