Comment on "Statistical Mechanics of Membrane-Protein Conformation: A Homopolymer Model"
Julian Juhi-Lian Ting
由于缺乏结构信息，最近一篇关于蛋白质-膜相互作用的论文的某些方面是不充分的。
Some aspects of a recent paper about protein-membrane interaction are inadequate due to lack of structural information.
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The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such proteins cause local deformations in the membrane, which induce an extra hydrodynamic drag on the protein. Using membrane tension to control the magnitude of the deformations and hence the drag, measurements of diffusivity can be used to infer--- via an elastic model of the protein--- how conformation is changed by tension. Motivated by recent experimental res…
We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering Monte Carlo simulations it is shown that the system exhibits a rich phase behavior ranging from highly ordered, compact to extended random coil structures and from desorbed to completely adsorbed or even partially embedded conformations. These findings are summarized in a pseudophase diagram indicating the predominant class of conformations as a function of the…
The shapes of cell membranes are largely regulated by membrane associated, curvature active, proteins. We use a numerical model of the membrane with elongated membrane inclusions, recently developed by us, which posses spontaneous directional curvatures that could be different along and perpendicular to its long axis. We show that, due to membrane mediated interactions these curvature inducing membrane nematogens can oligomerize spontaneously, even at low concentrations, and change the local shape of the membrane. We demonstrate that for a large group of such inclusions, where the two spontane…
A beam--membrane biomechanical vocal fold model incorporating posturing and glottal conformation
提出一种计算高效的梁-膜复合声带模型，通过模拟喉内肌激活对声带姿势和声门构型的影响，揭示不完全声门闭合对发声动力学的生物力学机制。
Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy landscape controlling the conformational transitions suffered by such proteins. For membrane channels, this effect can alter the critical membrane tension at which they undergo a transition from a closed to an open state, and therefore influence protein function \emph{in vivo}. Despite their obvious importance, crowding phenomena in membranes are much less well…
Photosensitive proteins embedded in the cell membrane (about 5 nm thickness) act as photoactivated proton pumps, ion gates, enzymes, or more generally, as initiators of stimuli for the cell activity. They are composed of a protein backbone and a covalently bound cofactor (e.g. the retinal chromophore in bacteriorhodopsin (BR), channel rhodopsin, and other opsins). The light-induced conformational changes of both the cofactor and the protein are at the basis of the physiological functions of photosensitive proteins. Despite the dramatic development of microscopy techniques, investigating confor…
Real-Time Analysis of Nanoscale Dynamics in Membrane Protein Insertion via Single-Molecule Imaging
本文提出SIFA和LipoFRET两种单分子成像方法，以亚纳米精度实时监测膜蛋白插入过程中的纳米尺度拓扑与构象动力学，解决了单个蛋白插入深度难以观测的问题。
Neutron Reflectometry Reveals Conformational Changes in a Mechanosensitive Protein Induced by an Antimicrobial Peptide in Tethered Lipid Bilayers
本研究利用中子反射法首次直接证明抗菌肽pexiganan可诱导机械敏感蛋白MscL的C末端突出部分发生构象变化，突出长度从约46 Å降至约38 Å。
The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been investigated in the past. We show, using Monte Carlo simulations, that the affinity of proteins for specific lipids can hasten its aggregation kinetics. The lipid membrane is modeled as a dynamically triangulated surface with the proteins defined as in-plane fields at the vertices. We show that, even at low protein concentrations, strong lipid-protein inter…
Over the past thirty years, researchers have highlighted the role played by a class of proteins or polypeptides that forms pathogenic amyloid aggregates in vivo, including i) the amyloid Abeta peptide, which is known to form senile plaques in Alzheimer's disease; ii) alpha-synuclein, responsible for Lewy body formation in Parkinson's disease and iii) IAPP, which is the protein component of type 2 diabetes-associated islet amyloids. These proteins, known as intrinsically disordered proteins (IDPs), are present as highly dynamic conformational ensembles. IDPs can partially (mis) fold into (dys) …
Mechanochemical action of the dynamin protein
发动蛋白是一种普遍存在的GTdR，其使脂质双层微管化，并且涉及真核细胞中的许多膜切割过程。为了更好地理解这种生物学功能，我们开发了一种广义的流体力学描述的构象变化的大型dynamin-membrane管考虑到GTP消耗作为一种自由能源。在可观察的时间尺度上，耗散主要由有效的dynamin/膜摩擦和管的变形场具有简单的扩散行为，这可以通过实验来测试。一个更复杂的，半微观模型产生完整的预测管的动力学，并可能占矛盾的实验结果，其构象的变化，以及plectonemic超螺旋。
High-resolution structural information on membrane proteins is essential for understanding cell biology and for structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide Ångstrom-level information about the structure of membrane proteins. Ideally protein structures should be solved in environments as close to the original biological context as possible. However, it is virtually impossible to crystallize proteins within the complex environment of a biological membrane. Instead, membrane proteins are typically transferred from their native memb…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight into the thermodynamics of membrane association we model the resulting alpha-helical structures as infinite rigid cylinders patterned with hydrophobic and hydrophilic stripes oriented parallel to their axis. Statistical thermodynamic calculations using Single Chain Mean Field (SCMF) theory show that the relative thickness of the stripes controls the free ener…
Interface-Driven Peptide Folding: Quantum Computations on Simulated Membrane Surfaces
本研究扩展现有量子计算算法，预测抗菌肽在类似脂质膜的亲水-疏水界面上的最佳构象，无需增加量子比特，展示了量子计算在复杂生物分子过程建模中的潜力。
It is crucial to measure position and conformational changes of a membrane-interacting protein relative to the membrane surface. This is however challenging because the thickness of a membrane is usually only about 4 nm. We developed a fluorescence method which makes use of the principle of FRET between a fluorophore and a cloud of quenchers encapsulated in a liposome, hence the name LipoFRET. LipoFRET can readily locate a fluorophore in different depths inside and at different heights above the membrane. We applied LipoFRET to study α-synuclein, a key player in the pathology of Parkinson's di…
Ever since the raft model for biomembranes has been proposed, the traditional view of biomembranes based on the fluid-mosaic model has been altered. In the raft model, dynamical heterogeneities in multi-component lipid bilayers play an essential role. Focusing on the lateral phase separation of biomembranes and vesicles, we review some of the most relevant research conducted over the last decade. We mainly refer to those experimental works that are based on physical chemistry approach, and to theoretical explanations given in terms of soft matter physics. In the first part, we describe the pha…
Modulating lipid membrane morphology by dynamic DNA origami networks
本研究提出可锚定巨型单层囊泡的DNA折纸十字结构，其能聚合为可重构的一维或二维网络，通过DNA燃料切换左右手构象以调控膜曲率，为合成细胞的可编程调控提供新方法。
Tilt-induced clustering of cell adhesion proteins
本文提出细胞黏附蛋白通过感知膜形变梯度（倾斜诱导）自发形成盘状和线状聚集结构，理论结果与实验估计一致。
Motivated to understand the behavior of biological filaments interacting with membranes of various types, we study a theoretical model for the shape and thermodynamics of intrinsically-helical filaments bound to curved membranes. We show filament-surface interactions lead to a host of non-uniform shape equilibria, in which filaments progressively unwind from their native twist with increasing surface interaction and surface curvature, ultimately adopting uniform-contact curved shapes. The latter effect is due to non-linear coupling between elastic twist and bending of filaments on anisotropica…
Tube geometry controls protein cluster conformation and stability on the endoplasmic reticulum surface
本研究通过动力学蒙特卡洛模拟发现，内质网管的粗细会调控IRE1蛋白簇的包裹构象，细管上的包裹态簇生长更快、更稳定，揭示了细胞器几何结构对未折叠蛋白反应信号的调控作用。
Membrane proteins typically deform the surrounding lipid bilayer membrane, which can play an important role in the function, regulation, and organization of membrane proteins. Membrane elasticity theory provides a beautiful description of protein-induced lipid bilayer deformations, in which all physical parameters can be directly determined from experiments. Analytic treatments of the membrane elasticity theory of protein-induced lipid bilayer deformations have largely focused on idealized protein shapes with circular cross section, and on perturbative solutions for proteins with non-circular …
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