scholarly journals Pressure effects on lipids and bio-membrane assemblies

IUCrJ ◽  
2014 ◽  
Vol 1 (6) ◽  
pp. 470-477 ◽  
Author(s):  
Nicholas J. Brooks
Keyword(s):  
High Pressure ◽  
Deep Sea ◽  
Lipid Membranes ◽  
Active Role ◽  
Pressure Effects ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Structure And Dynamics ◽  
Wide Range ◽  
Recent Developments

Membranes are amongst the most important biological structures; they maintain the fundamental integrity of cells, compartmentalize regions within them and play an active role in a wide range of cellular processes. Pressure can play a key role in probing the structure and dynamics of membrane assemblies, and is also critical to the biology and adaptation of deep-sea organisms. This article presents an overview of the effect of pressure on the mesostructure of lipid membranes, bilayer organization and lipid–protein assemblies. It also summarizes recent developments in high-pressure structural instrumentation suitable for experiments on membranes.

Artificial protein assemblies with well-defined supramolecular protein nanostructures

2021 ◽  
Author(s):  
Suyeong Han ◽  
Yongwon Jung
Keyword(s):  
Vaccine Development ◽  
De Novo ◽  
Building Blocks ◽  
Protein Assembly ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Wide Range ◽  
Array Structures ◽  
Small Chemical ◽  
Artificial Protein

Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.

scholarly journals Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4

2021 ◽  
Author(s):  
Tim Neijenhuis ◽  
Siri C. van Keulen ◽  
Alexandre M.J.J. Bonvin
Keyword(s):  
Protein Complexes ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Protein Interfaces ◽  
Density Maps ◽  
Medium Resolution ◽  
Wide Range ◽  
Multimeric Protein

A wide range of cellular processes require the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The produced density maps can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low-to-medium resolution maps. Unfortunately, the produced models frequently contain atomic clashes at the protein-protein interfaces (PPIs) as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best performing protocol, consisting of a semi-flexible simulated annealing refinement with restraints on the centroids of the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.

Multicomponent and High-Pressure Effects on Droplet Vaporization

2002 ◽  
Vol 124 (2) ◽  
pp. 248-255 ◽  
Author(s):  
S. K. Aggarwal ◽  
H. C. Mongia
Keyword(s):  
High Pressure ◽  
Gas Turbine ◽  
Single Component ◽  
Pressure Effects ◽  
Diffusion Limit ◽  
Fuel Droplet ◽  
Droplet Model ◽  
Droplet Vaporization ◽  
Wide Range ◽  
High Pressure Effects

This paper deals with the multicomponent nature of gas turbine fuels under high-pressure conditions. The study is motivated by the consideration that the droplet submodels that are currently employed in spray codes for predicting gas turbine combustor flows do not adequately incorporate the multicomponent fuel and high-pressure effects. The quasi-steady multicomponent droplet model has been employed to investigate conditions under which the vaporization behavior of a multicomponent fuel droplet can be represented by a surrogate pure fuel droplet. The physical system considered is that of a multicomponent fuel droplet undergoing quasi-steady vaporization in an environment characterized by its temperature, pressure, and composition. Using different vaporization models, such as infinite-diffusion and diffusion-limit models, the predicted vaporization history and other relevant properties of a bicomponent droplet are compared with those of a surrogate single-component fuel droplet over a range of parameters relevant to gas turbine combustors. Results indicate that for moderate and high-power operation, a suitably selected single-component (50 percent boiling point) fuel can be used to represent the vaporization behavior of a bicomponent fuel, provided one employs the diffusion-limit or effective-diffusivity model. Simulation of the bicomponent fuel by a surrogate fuel becomes increasingly better at higher pressures. In fact, the droplet vaporization behavior at higher pressures is observed to be more sensitive to droplet heating models rather than to liquid fuel composition. This can be attributed to increase in the droplet heatup time and reduction in the volatility differential between the constituent fuels at higher pressures. For ignition, lean blowout and idle operations, characterized by low pressure and temperature ambient, the multicomponent fuel evaporation cannot be simulated by a single-component fuel. The validity of a quasi-steady high-pressure droplet vaporization model has also been examined. The model includes the nonideal gas behavior, liquid-phase solubility of gases, and variable thermo-transport properties including their dependence on pressure. Predictions of the high-pressure droplet model show good agreement with the available experimental data over a wide range of pressures, implying that quasi-steady vaporization model can be used at pressures up to the fuel critical pressure.

Aggregation of amyloids in a cellular context: modelling and experiment

2011 ◽  
Vol 438 (3) ◽  
pp. 415-426 ◽  
Author(s):  
Ran Friedman
Keyword(s):  
Lipid Membranes ◽  
Amyloid Β ◽  
Integrative Approach ◽  
Aggregation Process ◽  
Amyloid Aggregation ◽  
Molecular Events ◽  
Context Modelling ◽  
Wide Range ◽  
Recent Developments

Amyloid-related diseases are a group of illnesses in which an abnormal accumulation of proteins into fibrillar structures is evident. Results from a wide range of studies, ranging from identification of amyloid-β dimers in the brain to biophysical characterization of the interactions between amyloidogenic peptides and lipid membranes during fibril growth shed light on the initial events which take place during amyloid aggregation. Accounts of fibril disaggregation and formation of globular aggregates due to interactions with lipids or fatty acids further demonstrate the complexity of the aggregation process and the difficulty to treat amyloid-related diseases. There is an inherent difficulty in generalizing from studies of aggregation in vitro, but the involvement of too many cellular components limits the ability to follow amyloid aggregation in a cellular (or extracellular) context. Fortunately, the development of experimental methods to generate stable globular aggregates suggests new means of studying the molecular events associated with amyloid aggregation. Furthermore, simulation studies enable deeper understanding of the experimental results and provide useful predictions that can be tested in the laboratory. Computer simulations can nowadays provide molecular or even atomistic details that are experimentally not available or very difficult to obtain. In the present review, recent developments on modelling and experiments of amyloid aggregation are reviewed, and an integrative account on how isolated interactions (as observed in vitro and in silico) combine during the course of amyloid-related diseases is presented. Finally, it is argued that an integrative approach is necessary to get a better understanding of the protein aggregation process.

scholarly journals Biologische Festkörper-NMR-Spektroskopie in der Strukturbiologie

BIOspektrum ◽  
2021 ◽  
Vol 27 (3) ◽  
pp. 257-259
Author(s):  
Nils-Alexander Lakomek
Keyword(s):  
Solid State Nmr ◽  
Structural Information ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Structure And Dynamics ◽  
Wide Range ◽  
Recent Developments ◽  
Lipid Environment ◽  
Angle Spinning ◽  
Fast Magic Angle Spinning

AbstractBiological solid-state NMR elucidates the structure and dynamics of biomolecules at physiological temperatures. It provides high-resolution structural information for a wide range of biomolecules and assemblies, from small membrane proteins embedded in a lipid environment, over fibrillar structures up to supramolecular assemblies. Recent developments allow for proton detection at fast magic angle spinning frequencies, which reduces the required sample amounts to a few hundreds of micrograms.

scholarly journals Assessing the use of ellipsoidal microparticles for determining lipid membrane viscosity

2021 ◽  
Author(s):  
Philip E. Jahl ◽  
Raghuveer Parthasarathy
Keyword(s):  
Lipid Membranes ◽  
Lipid Membrane ◽  
Translational Diffusion ◽  
Lipid Domains ◽  
Giant Vesicles ◽  
Membrane Viscosity ◽  
Cellular Processes ◽  
Wide Range ◽  
Chain Lengths ◽  
Good Agreement

The viscosity of lipid membranes sets the timescales of membrane-associated flows and therefore influences the dynamics of a wide range of cellular processes. Techniques to measure membrane viscosity remain sparse, however, and reported measurements to date, even of similar systems, give viscosity values that span orders of magnitude. To address this, we improve a method based on measuring both the rotational and translational diffusion of membrane-anchored microparticles and apply this approach and one based on tracking the motion of phase-separated lipid domains to the same system of phase-separated giant vesicles. We find good agreement between the two methods, with inferred viscosities within a factor of two of each other. Our technique uses ellipsoidal microparticles, and we show that the extraction of physically meaningful viscosity values from their motion requires consideration of their anisotropic shape. The validation of our method on phase-separated membranes makes possible its application to other systems, which we demonstrate by measuring the viscosity of bilayers composed of lipids with different chain lengths ranging from 14 to 20 carbon atoms, revealing a very weak dependence of two-dimensional viscosity on lipid size. The experimental and analysis methods described here should be generally applicable to a variety of membrane systems, both reconstituted and cellular.

High-Pressure Effects on the Structure and Phase Behavior of Model Membrane Systems

1996 ◽  
Author(s):  
Roland Winter ◽  
Anne Landwehr
Keyword(s):  
High Pressure ◽  
Phase Behavior ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Membrane Lipids ◽  
Pressure Effects ◽  
Scanning Calorimetry ◽  
Hydrocarbon Chains ◽  
Temperature And Pressure ◽  
Lipid Conformation

Phospholipids, which provide valuable model systems for lipid membranes, display a variety of polymorphic phases, depending on their molecular structure and on environmental conditions. High hydrostatic pressure has been used as a physical parameter to study the thermodynamic properties and phase behavior of these systems. High pressure is also a characteristic feature of certain natural membrane environments. In the first part of this article, we review our recent work on the temperature- and pressure-dependent phase behavior of phospholipid systems differing in lipid conformation and headgroup structure. In the second part, we report on the determination of the (T, x, p) phase diagrams of binary phospholipid mixtures. An additional section deals with effects of incorporating ions, small amphiphilic molecules, and steroids into the bilayer on the experimental temperature- and pressure-dependent phase behavior of lipid systems. Finally, we discuss lamellar to nonlamellar thermotropic and barotropic phase transformations, which occur for a number of lipids, such as phosphatidylethanolamines, monoacylglycerides, and lipid mixtures. It has been suggested that nonlamellar lipid structures might play an important role as transient and local intermediates in a number of biochemical processes. High-pressure smallangle x-ray (SAXS) and neutron (SANS) scattering, differential scanning calorimetry (DSC), high-pressure differential thermal analysis (DTA), and p, V, T measurements have been used as experimental methods for the investigation of these systems. Lipid bilayer dispersions, in particular the phosphatidylcholines and phosphatidylethanolamines, are the workhorses for the investigation of biophysical properties of membrane lipids because they constitute the basic structural component of biological membranes. They exhibit a rich lyotropic and thermotropic phase behavior (Cevc & Marsh, 1987; Marsh, 1991; Yeagle, 1992). Most fully hydrated saturated phospholipid bilayers exhibit two principal thermotropic lamellar phase transitions, corresponding to a gel to gel (Lβ′–Pβ′) transition and a gel to liquid-crystalline (Pβ′–Lα) main transition at a temperature Tm. In the fluid-like La phase, the hydrocarbon chains of the lipid bilayers are conformationally disordered, whereas in the gel phases the hydrocarbon chains are more extended and relatively ordered.

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