Quaternary dynamics and plasticity underlie small heat shock protein chaperone function

Small Heat Shock Proteins (sHSPs) are a diverse family of molecular chaperones that prevent protein aggregation by binding clients destabilized during cellular stress. Here we probe the architecture and dynamics of complexes formed between an oligomeric sHSP and client by employing unique mass spectrometry strategies. We observe over 300 different stoichiometries of interaction, demonstrating that an ensemble of structures underlies the protection these chaperones confer to unfolding clients. This astonishing heterogeneity not only makes the system quite distinct in behavior to ATP-dependent chaperones, but also renders it intractable by conventional structural biology approaches. We find that thermally regulated quaternary dynamics of the sHSP establish and maintain the plasticity of the system. This extends the paradigm that intrinsic dynamics are crucial to protein function to include equilibrium fluctuations in quaternary structure, and suggests they are integral to the sHSPs’ role in the cellular protein homeostasis network.     

Multistart simulated annealing refinement of the crystal structure of the 70S ribosome

A macromolecular X-ray crystal structure is usually represented as a single static model with a single set of temperature factors representing a simple approximation of motion and disorder of the structure. Multiconformer representations of small proteins have been shown to better describe anisotropic motion and disorder and improve the quality of their electron density maps. Here, we apply multistart simulated annealing crystallographic refinement to a 70S ribosome-RF1 translation termination complex that was recently solved at 3.2 Å resolution. The analysis improves the interpretability of the electron density map of this 2.5-MDa ribonucleoprotein complex and provides insights into its structural dynamics. We also used multistart refinement and conventional Fourier difference maps to address a recent study in which cross-crystal averaging between two crystal forms of the 70S ribosome was used to evaluate reported differences between two ribosome crystal structures solved at 2.8 and 3.7 Å resolution. Our analysis suggests that results obtained from cross-crystal averaging are inherently biased toward the higher-resolution dataset.     

Dynamic structure of lipid-bound synaptobrevin suggests a nucleation-propagation mechanism for trans-SNARE complex formation

The synaptic vesicle protein synaptobrevin engages with syntaxin and SNAP-25 to form the SNARE complex, which drives membrane fusion in neuronal exocytosis. In the SNARE complex, the SNARE motif of synaptobrevin forms a 55-residue helix, but it has been assumed to be mostly unstructured in its prefusion form. NMR data for full-length synaptobrevin in dodecylphosphocholine micelles reveals two transient helical segments flanked by natively disordered regions and a third more stable helix. Transient helix I comprises the most N-terminal part of the SNARE motif, transient helix II extends the SNARE motif into the juxtamembrane region, and the more stable helix III is the transmembrane domain. These helices may have important consequences for SNARE complex folding and fusion: helix I likely forms a nucleation site, the C-terminal disordered SNARE motif may act as a folding arrest signal, and helix II likely couples SNARE complex folding and fusion.     

Experimental test of a predicted dynamics–structure–thermodynamics connection in molecularly complex glass-forming liquids

Understanding in a unified manner the generic and chemically specific aspects of activated dynamics in diverse glass-forming liquids over 14 or more decades in time is a grand challenge in condensed matter physics, physical chemistry, and materials science and engineering. Large families of conceptually distinct models have postulated a causal connection with qualitatively different “order parameters” including various measures of structure, free volume, thermodynamic properties, short or intermediate time dynamics, and mechanical properties. Construction of a predictive theory that covers both the noncooperative and cooperative activated relaxation regimes remains elusive. Here, we test using solely experimental data a recent microscopic dynamical theory prediction that although activated relaxation is a spatially coupled local–nonlocal event with barriers quantified by local pair structure, it can also be understood based on the dimensionless compressibility via an equilibrium statistical mechanics connection between thermodynamics and structure. This prediction is found to be consistent with observations on diverse fragile molecular liquids under isobaric and isochoric conditions and provides a different conceptual view of the global relaxation map. As a corollary, a theoretical basis is established for the structural relaxation time scale growing exponentially with inverse temperature to a high power, consistent with experiments in the deeply supercooled regime. A criterion for the irrelevance of collective elasticity effects is deduced and shown to be consistent with viscous flow in low-fragility inorganic network-forming melts. Finally, implications for relaxation in the equilibrated deep glass state are briefly considered.

An enormous number of seemingly orthogonal proposals exist for a fundamental connection between a (typically scalar) structural or excess (configurational) thermodynamic quantity and activated relaxation in supercooled liquids (1–12). High chemical complexity for fragile glass formers which exhibit strongly non-Arrhenius relaxation greatly complicates the formulation of predictive theories. A common generic view (1, 3, 8) is that the structural or alpha relaxation time (and viscosity, inverse diffusivity) evolves with cooling as shown in Fig. 1A. Different dynamical mechanisms in the high-, intermediate-, and low-temperature regimes are often envisioned: noncooperative Arrhenius (∼1 ps to 100 ps), critical power law (∼0.1 ns to 100 ns), and cooperative non-Arrhenius (∼0.1 μs to 100 s or beyond), respectively. Typically a causal connection is postulated between the logarithm of the alpha time (an effective barrier in thermal energy units) and a specific “order parameter”: 1) in the structural class (6, 7, 13–17), the intensity of the cage peak of the structure factor S(k), local aspect(s) of the radial distribution function g(r), or specific packing motifs; 2) in the thermodynamics class, various measures of free volume (18, 19), excess entropy (20), configurational entropy (21–25), internal energy and enthalpy (26), or with some arguing for an equilibrium phase transition at an inaccessibly low (high) temperature (density) (23, 27–29); 3) in the short time class, the high-frequency shear modulus (2, 30–32), Debye–Waller factor (33), or amplitude of special vibrational modes (33–35); and 4) in the intermediate time class, the concentration of dilute mobile excitations [e.g., strings (36, 37) or facilitating defects (38)]. Many of the proposed order parameters are hard or impossible to uniquely define and/or experimentally measure. The diverse models often claim to capture relaxation data over limited time windows typically based on fitting but usually fail at low and/or high enough temperature (5).Open in a separate windowFig. 1.Global relaxation map and theoretical picture and key predictions. (A) Three-regime relaxation map (curves) for the alpha time with Arrhenius and strongly non-Arrhenius behaviors separated by a crossover regime perhaps of a critical power law (6) form. The proposed two-regime scenario of ECNLE theory (39–42) is based solely on noncooperative and cooperative activated dynamics (slightly overlapping orange and green regions) with the inverse dimensionless compressibility (S0−1) as the relevant thermodynamic quantity. The approximately five to six decade range that simulations can probe is indicated. (B) Dynamic free energy for a metastable hard sphere (diameter σ) fluid (42) as a function of particle displacement at a high packing fraction of ϕ = 0.58. Relevant length and energy scales are indicated. (Inset) Schematic of the core physical idea for the alpha relaxation: hopping on the cage scale coupled with a collective elastic displacement of all particles outside the cage. (C) Main: local cage barrier as a function of inverse dimensionless compressibility for 0.44<ϕ <0.61 corresponding to a 16 decade increase of the alpha time (39, 41, 42). The metastable regime begins at ϕ ∼ 0.5 where the total barrier is ∼1.5 k_BT. (Inset) Total barrier as a function of S0−3 normalized by its ϕ = 0.5 value. The elastic barrier is 1 k_BT at ϕ ∼ 0.55. Packing fractions are given along the top x-axis.Here we present, using only experimental data, a test of a relationship between activated relaxation, local pair structure, and a specific thermodynamic property predicted by the Elastically Collective Nonlinear Langevin Equation (ECNLE) theory (39–41). The results provide support for the following: 1) the coupled local–nonlocal nature of relaxation deeply connected with collective elasticity, 2) the dimensionless amplitude of thermal density fluctuations, S₀, as the relevant (nonexcess) thermodynamic property, 3) a roadmap for organizing relaxation data in S₀, not in temperature, space, 4) irrelevance of collective elasticity as the origin for the crossover from fragile to strong glass formers, and 5) an explicit demonstration that a dynamics–thermodynamics correlation can be a noncausal consequence of the causal relation between local pair structure and S₀.     

Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation

The CA (capsid) domain of immature HIV-1 Gag and the adjacent spacer peptide 1 (SP1) play a key role in viral assembly by forming a lattice of CA hexamers, which adapts to viral envelope curvature by incorporating small lattice defects and a large gap at the site of budding. This lattice is stabilized by intrahexameric and interhexameric CA-CA interactions, which are important in regulating viral assembly and maturation. We applied subtomogram averaging and classification to determine the oligomerization state of CA at lattice edges and found that CA forms partial hexamers. These structures reveal the network of interactions formed by CA-SP1 at the lattice edge. We also performed atomistic molecular dynamics simulations of CA-CA interactions stabilizing the immature lattice and partial CA-SP1 helical bundles. Free energy calculations reveal increased propensity for helix-to-coil transitions in partial hexamers compared to complete six-helix bundles. Taken together, these results suggest that the CA dimer is the basic unit of lattice assembly, partial hexamers exist at lattice edges, these are in a helix-coil dynamic equilibrium, and partial helical bundles are more likely to unfold, representing potential sites for HIV-1 maturation initiation.

The polyprotein Gag is the main structural component of HIV-1, consisting of the MA (matrix), CA (capsid), NC (nucleocapsid), and p6 domains as well as the spacer peptides SP1 and SP2 (1). Gag is produced in infected host cells and trafficked to the plasma membrane, where it assembles into a hexagonal lattice via its CA domain and recruits other viral proteins and the viral RNA genome (1, 2). Assembly of the curved Gag lattice is commensurate with membrane bending at the site of assembly, after which recruitment of Endosomal Sorting Complex Required for Transport III (ESCRT-III) components by the p6 domain of Gag induces membrane scission and release of the immature virus particle (2). The hexagonal Gag lattice accommodates curvature in the growing bud by incorporating vacancy defects (3). The activity of ESCRT-III is timed such that the final immature lattice is incomplete, giving rise to an additional large gap in the lattice, resulting in a truncated spherical shape (4–6).During or after budding, the viral protease is activated and cleaves this immature Gag lattice into its component domains, which leads to structural rearrangement within the virus particle (2). The released CA domains assemble to form a closed, conical capsid around the condensed ribonucleoprotein (RNP) complex of the mature virus (1, 7). Maturation is required for the virion to become infectious (1).Within the immature virus particle, the N-terminal domain of CA (CA_NTD) forms trimeric interactions linking three Gag hexamers while the C-terminal domain of CA (CA_CTD) forms dimeric interactions mediated by helix 9 of CA, linking two Gag hexamers together (8). The CA_CTD additionally forms intrahexamer interactions around the sixfold axis of the hexamer (8, 9). Amphipathic helices formed by the C-terminal residues of CA_CTD and the N-terminal residues of SP1 junction assemble into a six-helix bundle (6HB), thereby imposing hexagonal order on the CA domains, via classical knobs-in-holes packing mediated by exposed hydrophobic side chains, as also seen in coiled coils (9, 10). In combination, these relatively weak interactions give rise to a very dynamic, reversible assembly process that prevents the assembling lattice from becoming trapped in kinetically unfavorable states (11). This robust assembly behavior is consistent with icosahedral viruses (12–15). It is not surprising, therefore, that the energetics of Gag assembly are tightly controlled and highly dependent on scaffolding effects from the viral RNA and the membrane-interacting MA domain of Gag in order to ensure productive viral assembly (11, 16). Analysis of the diffusion pattern of fluorescently labeled Gag supports the notion that Gag is trafficked to the site of assembly as low-order multimers, although it is still unclear whether these are Gag dimers, trimers, or other multimeric forms of Gag (16, 17).The primary assembly unit of the Gag lattice remains largely unknown. We can identify two hypothetical ways in which the lattice could assemble. First, the lattice could grow by addition of Gag hexamers (or sets of six component monomers), such that the CA-SP1 junction is assembled within a hexameric 6HB at all positions in the lattice. In this case, interfaces between hexamers would be unoccupied at the edge of the lattice. From a purely energetic perspective, this appears most reasonable. Second, the lattice could form via addition of Gag dimers or Gag trimers (or equivalently from sets of either two or three component monomers). This would maintain, for example, the dimeric CA-CA interhexamer interactions but leave incomplete hexamers at the lattice edges, including unoccupied hexamer-forming interfaces along the CA-SP1 bundle. It additionally remains unclear whether the unoccupied Gag-Gag interfaces at the lattice edges are simply exposed, or whether they are stabilized by alternative conformations of individual domains or proteins, or by other binding partners. Understanding the structure of the edge of the immature Gag lattice therefore has implications for understanding the mechanism of virus assembly.Viral assembly, budding, and maturation are tightly linked, and disrupting the kinetics of any of these processes can give rise to defects in maturation and formation of noninfectious viral particles (1, 18, 19). The rate-limiting proteolytic cleavage site in the maturation process resides within the CA-SP1 6HB (20). Unfolding of the helical bundle is required to allow proteolytic cleavage to proceed (21–23), but the exact mechanism for protease access to this site is not known. The spatial localization of proteolytic processing within the context of the immature Gag lattice is relevant: Does the protease act on Gag within the lattice, or does it act on the edges of the Gag lattice, causing a cascade of lattice disruption? At the lattice edge, is the substrate for the protease with a 6HB or within an incomplete hexamer? Understanding the structure of the edge of the immature Gag lattice therefore has implications for understanding the mechanism of virus maturation.High-resolution immature Gag structures have previously been determined directly from purified viruses by cryo-electron tomography (cryo-ET) and subtomogram averaging (10). These structures represent an average hexamer within the immature lattice, with a full complement of six Gag hexamer neighbors. Here, we have applied subtomogram classification and averaging approaches to an existing immature virus dataset (10) in order to determine the structures of Gag assemblies at lattice edges. We also applied atomistic molecular dynamics simulations to assess the roles of the different CA-CA interactions in immature lattice stabilization and predict the properties of the structures we observe at lattice edges. Together, our results suggest that the basic unit of immature HIV-1 assembly is a Gag dimer and partial CA-SP1 helical bundles are present at the edges of the assembled lattice and may be substrates for initiation of maturation.     

采用分子动力学模拟探究VWF-A1突变体G561S的亲和力变化机制

目的探究血管性血友病因子(von Willebrand factor,VWF)突变体G561S下调VWF-A1与其配体亲和力的分子机制。方法分别构建2M型突变体G561S-A1(功能减弱型)、WT-A1(野生型)和2B型突变体R543Q-A1(功能增强型)3个分子系统。G561S-A1突变体采用将野生型A1结构的Gly561替换为Ser561的方式构建,WT-A1与R543Q-A1晶体结构取自蛋白质数据库(protein data bank,PDB)。利用自由分子动力学模拟方法对比分析WT-A1、G561S-A1、R543Q-A1三者构象的改变、柔性的变化以及氢键/盐桥的形成与演化。结果 G561S突变通过降低A1结构域α2螺旋的柔性,并增强N末端与body区的相互作用从而减弱其与配体GPIbα的亲和力,R543Q功能增强型突变体则启动了一条相反的调节路径。结论局部动力学性质的改变是A1亲和力调控的潜在机制,研究结果有助于针对激活的A1结构域的变构药物设计以及相关抗血栓药物的研发。     

A fluorescent probe designed for studying protein conformational change

The usefulness of fluorescence in studying protein motions derives from its sensitivity, kinetic resolution, and compatibility with both live cells and physiological assays. Recent advances in microscopy and membrane protein purification have permitted the observation of fluorescence changes that accompany the functional transitions of complex eukaryotic membrane proteins. These techniques rely on probes that can clearly report the environmental changes of specific residues, but most commonly available side-chain-reactive probes are not well suited for this purpose. Here, we introduce a red Cys-reactive probe, aminophenoxazone maleimide (APM), designed with improved chemical and spectral properties for reporting protein conformational change. APM is compact, uncharged, and has a short linker between probe and protein, all of which ensure that it can closely track the motions of the side chain to which it is attached. It undergoes large polarity-dependent changes in Stokes shift, as well as large bathochromic shifts in both excitation maximum (from 521 nm in toluene to 598 nm in water) and emission maximum (580 nm to 633 nm). These polarity-dependent spectral changes offer a potentially simple means of relating fluorescence to local structure and motion, although they are partially offset by some complicating factors in APM fluorescence. We find that, like a rhodamine maleimide, APM senses the conformational changes underlying voltage sensing in the Shaker potassium channel, and it is superior at a site that shows limited reactivity to the rhodamine. The spectral characteristics of APM can also report subtle differences between aqueous positions in purified preparations of the beta2 adrenergic receptor.