Elasticity of the Transition State Leading to an Unexpected Mechanical Stabilization of Titin Immunoglobulin Domains

The giant protein titin plays a critical role in regulating the passive elasticity of muscles, mainly through the stochastic unfolding and refolding of its numerous immunoglobulin domains in the I‐band of sarcomeres. The unfolding dynamics of titin immunoglobulin domains at a force range greater than 100 pN has been studied by atomic force microscopy, while that at smaller physiological forces has not been measured before. By using magnetic tweezers, it is found that the titin I27 domain unfolds in a surprising non‐monotonic force‐dependent manner at forces smaller than 100 pN, with the slowest unfolding rate occurring around 22 pN. We further demonstrate that a model with single unfolding pathway taking into account the elasticity of the transition state can reproduce the experimental results. These results provide important novel insights into the regulation mechanism of the passive elasticity of muscle tissues.     

Versal Deformations in Spaces of Polynomials of Fixed Weight

This work was largely inspired by a paper of Shustin, in which he proves that for a plane curve of given degree n whose singularities are not too complicated the singularities are versally unfolded by embedding the curve in the space of all curves of degree n; however, our methods are very different. The main result gives fairly explicit lower bounds on the sum of the Tjurina numbers at the singularities of a deformation of a weighted-homogeneous hypersurface, when the deformation is the fibre over an unstable point of an appropriate unfolding. The result is sufficiently flexible to cover a variety of applications, some of which we describe. In particular, we will deduce a generalisation of Shustin's result. Properties of discriminant matrices of unfoldings of weighted-homogeneous functions are crucial to the arguments; the parts of the theory needed are described.     

Membrane-bound Na+,K+-ATPase as the cardiac glycoside receptor

DSC studies are carried out to characterize Na⁺,K⁺-ATPase isolated from pig kidney in its natural membrane environment as well as in its purified state upon detergent treatment. The transition temperatures of the investigated thermal protein unfolding process, observed between 43 and 64.5° C, depend on the local membrane environment as well as onpH. In addition, the transition temperature is significantly increased upon binding of different cations and ligands which are known to interact with the enzyme. Evidence for a lipid phase transition around 23 °C in the original biological membrane is reported.The application of a calorimeter equipped with removable cells appears to be more suitable for the investigation of this type of membrane sample than an instrument with fixed capillary cells. Filling the sample capillary cell with an usual syringe, consisting of a long and thin needle, can influence the experimental results.Na⁺, K⁺ -ATPase acts as the receptor for cardiac glycoside binding. The thermodynamic parameters of this binding process are determined by titration calorimetry. The binding of ouabain, as a typical example, is unusually slow and is enthalpy driven. The enthalpy change upon binding enthalpy is –75 kJ mol^–1 at 25 °C. The surprisingly low stoichiometric coefficient, resulting from an evaluation based on a simple one step binding model, is interpreted in terms of a dimeric receptor unit.The authors are grateful to E. Lewitzki, H. Ruf, E. Schick and F. Thommen for stimulating discussions, to A. Schacht for skilfull enzyme preparations and to the German Research Foundation for financial support (SFB 169).     

脲和盐酸胍诱导过氧化氢酶去折叠的研究

用荧光相图法分别研究了脲和盐酸胍诱导牛肝过氧化氢酶去折叠的过程。当脲 浓度从0依次增大至0.50,4.5和8.0 mol/L时,过氧化氢酶从天然四聚体依次转变 为蓬松的四聚体、部分折叠的无活性二聚体和去折叠态,而当盐酸胍浓度从0依次 变化至0.65,2.5和6.0 mol/L时,过氧化氢酶则从天然四聚体集资转变为部分折叠 的激活二聚体、部分折叠的单体和去折叠态,这表明无论是用脲还是用盐酸胍作为 变性剂,该蛋白的变性过程都符合“四态模型”,但这两种变性剂诱导该蛋白去折 叠的途径和机制有较大差异。实验结果表明荧光相图法可以检测蛋白质去折叠的中 间态。用等温滴定量去热法研究了盐酸胍诱导过氧化氢酶去折叠过程的热力学, 25.0 ℃时低浓度盐酸胍诱导该蛋白从天然四聚体转变为部分折叠的激活二聚体的 本征摩尔构象变化焓、Gibbs自由能和熵分别为-69.2 kJ·mol~(-1),6.43 kJ· mol~(-1)和-254 J·K~(-1)·mol~(-1),据此推断盐酸胍通过熵效应和静电效应来 稳定和激活该二聚体。     

Hierarchical Unfolding of Mj HSP16.5

Mj HSP16.5 is a small heat shock protein (sHSP) from the hyperthermophilic methanoarchaeon, Methanococcus jannaschii (Mj), which lives at the environment of high temperature up to 94 °C. The structural data showed that Mj HSP16.5 was a 24-mer that formed a hollow sphere with octahedral symmetry. Mj HSP16.5 was very stable at pH 7 that it maintained the 24-mer structure even at 85 °C. In the present study, we investigated the unfolding process of Mj HSP16.5 in the presence of denaturants using several techniques, including circular dichroism (CD), dynamic light scattering (DLS), fluorescence spectroscopy, and size exclusive chromatography (SEC). We found that 8 mol·L⁻¹ urea had no obvious effect on the structure of Mj HSP16.5 at pH 7. The unfolding of Mj HSP16.5 at pH 7 in the presence of guanidine hydrochloride (GdHCl) showed hierarchical behavior. Three significant transitions were observed around 2.0, 3.0, and 6.0 mol·L⁻¹ GdHCl at pH 7. ANS (8-anilino-1- naphthalenesulfonic acid) titration results showed that the binding ability of Mj HSP16.5 to ANS decreased gradually as the concentration of GdHCl increased until around 2.0 mol·L⁻¹ GdHCl, indicating surface hydrophobic area change, and this first transition was companioned with precipitation of Mj HSP16.5. Acrylamide quenching of fluorescence showed that the Stern-Volmer constant changed at about 3.0 mol·L⁻¹ GdHCl, indicating changes of the dimeric interface, and this phase transition was companioned with oligomeric state change from 24-mer to small oligomers (4-mer to 8-mer). The last unfolding phase started around 5.0 mol·L⁻¹ GdHCl, with a midpoint of 6.1 mol·L⁻¹ GdHCl, and Mj HSP16.5 was completely unfolded at 7.0 mol·L⁻¹ GdHCl. We also found that Mj HSP16.5 could be quite easily unfolded at pH 3, where it could be completely unfolded in 4.0 mol·L⁻¹ GdHCl.     

Grid Vertex-Unfolding Orthogonal Polyhedra

An edge-unfolding of a polyhedron is produced by cutting along edges and flattening the faces to a net, a connected planar piece with no overlaps. A grid unfolding allows additional cuts along grid edges induced by coordinate planes passing through every vertex. A vertex-unfolding allows faces in the net to be connected at single vertices, not necessarily along edges. We show that any orthogonal polyhedra of genus zero has a grid vertex-unfolding. (There are orthogonal polyhedra that cannot be vertex-unfolded, so some type of “gridding” of the faces is necessary.) For any orthogonal polyhedron P with n vertices, we describe an algorithm that vertex-unfolds P in O(n ²) time. Enroute to explaining this algorithm, we present a simpler vertex-unfolding algorithm that requires a 3×1×1 refinement of the vertex grid. This is a significant revision of the preliminary version that appeared in [2]. J. O’Rourke’s research was supported by NSF award DUE-0123154.     

Mpro-C蛋白三维结构域交换的机理: 来自分子模拟的线索

SARS冠状病毒主蛋白酶(M^pro)在病毒的蛋白酶切过程中发挥着重要作用. M^pro的晶体结构显示它存在两种形式的二聚体: 一种是发生三维结构域交换的形式, 另一种是非交换的形式. M^pro的C端结构域(M^pro-C)单独表达时也能形成与全长M^pro类似的三维结构域交换二聚体. 三维结构域交换通常发生在蛋白质的表面, 但M^pro-C 的结构域交换却发生在疏水核心. 在本文中, 我们利用分子动力学模拟及三维结构域交换预测算法研究了M^pro-C 中被高度埋藏的核心螺旋片段发生交换的机理. 我们发现基于结构与基于序列的已有算法都不能正确预言出M^pro-C和M^pro中发生结构域交换的铰链区位置. 分子模拟结果表明M^pro-C中的交换片段在天然态下埋藏得很好, 但在变性单体中则会被释放并暴露在外面. 因此, 在完全或部分解折叠状态下交换片段的打开有助于促进单体间的相互作用及结构域交换二聚体的形成.     

Dynamic control of protein conformation transition in chromatographic separation based on hydrophobic interactions: Molecular dynamics simulation

Conformational transitions of a protein in hydrophobic interaction based chromatography, including hydrophobic interaction chromatography (HIC) and reversed-phase liquid chromatography (RPLC), and their impact on the separation process and performance were probed by molecular dynamics simulation of a 46-bead β-barrel coarse-grained model protein in a confined pore, which represents the porous adsorbent. The transition of the adsorbed protein from the native conformation to an unfolded one occurred as a result of strong hydrophobic interactions with the pore surface, which reduced the formation of protein aggregates. The conformational transition was also displayed in the simulation once an elution buffer characterized by weaker hydrophobicity was introduced to strip protein from pore surface. The discharged proteins that underwent conformational transition were prone to aggregation; thus, an unsatisfactory yield of the native protein was obtained. An orthogonal experiment revealed that in addition to the strengths of the protein–protein and protein–adsorbent hydrophobic interactions, the elution time required to reduce the above-mentioned interactions also determined the yield of native protein by HIC and RPLC. Stepwise elution, characterized by sequential reduction of the hydrophobic interactions between the protein and adsorbent, was presented as a dynamic strategy for tuning conformational transitions to favor the native conformation and reduce the formation of protein aggregates during the elution process. The yield of the native protein obtained by this dynamic operation strategy was higher than that obtained by steady-state elution. The simulation study qualitatively reproduced the experimental observations and provided molecular insight that would be helpful for designing and optimizing HIC and RPLC separation of proteins.