The structure of insulin at the air/water interface: monomers or dimers?

Do Machine-Learning Atomic Descriptors and Order Parameters Tell the Same Story? The Case of Liquid Water

Machine-learning (ML) has become a key workhorse in molecular simulations. Building an ML model in this context involves encoding the information on chemical environments using local atomic descriptors. In this work, we focus on the Smooth Overlap of Atomic Positions (SOAP) and their application in studying the properties of liquid water both in the bulk and at the hydrophobic air-water interface. By using a statistical test aimed at assessing the relative information content of different distance measures defined on the same data space, we investigate if these descriptors provide the same information as some of the common order parameters that are used to characterize local water structure such as hydrogen bonding, density, or tetrahedrality to name a few. Our analysis suggests that the ML description and the standard order parameters of the local water structure are not equivalent. In particular, a combination of these order parameters probing local water environments can predict SOAP similarity only approximately, and vice versa, the environments that are similar according to SOAP are not necessarily similar according to the standard order parameters. We also elucidate the role of some of the metaparameters in the SOAP definition in encoding chemical information.

Strategies for interference of insulin fibrillogenesis: challenges and advances

The discovery of insulin came up with very high hopes for diabetic patients. In the year 2021, the world celebrated the 100 th anniversary of the discovery of this vital hormone. However, external use of insulin is highly affected by its aggregating tendency that occurs during its manufacturing, transportation, and improper handling which ultimately leads its pharmaceutically and biologically ineffective form. In this review, we aim to discuss the various approaches used for decelerating insulin aggregation which results in the enhancement of its overall structural stability and usage. The approaches that are discussed are broadly classified as either a measure through excipient additions or by intrinsic modifications in the insulin native structure.

Membrane Structure of Aquaporin Observed with Combined Experimental and Theoretical Sum Frequency Generation Spectroscopy

High-resolution structural information on membrane proteins is essential for understanding cell biology and for the structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide angstrom-level information about the structure of membrane proteins, yet for XRD experiments, proteins are removed from their native membrane environment, chemically stabilized, and crystallized, all of which can compromise the conformation. Here, we describe how a combination of surface-sensitive vibrational spectroscopy and molecular dynamics simulations can account for the native membrane environment. We observe the structure of a glycerol facilitator channel (GlpF), an aquaporin membrane channel finely tuned to selectively transport water and glycerol molecules across the membrane barrier. We find subtle but significant differences between the XRD structure and the inferred in situ structure of GlpF.

Human Apolipoprotein A1 at Solid/Liquid and Liquid/Gas Interfaces

An X-ray reflectivity study on the adsorption behavior of human apolipoprotein A1 (apoA1) at hydrophilic and hydrophobic interfaces is presented. It is shown that the protein interacts via electrostatic and hydrophobic interactions with the interfaces, resulting in the absorption of the protein. pH dependent measurements at the solid/liquid interface between silicon dioxide and aqueous protein solution show that in a small pH range between pH 4 and 6, adsorption is increased due to electrostatic attraction. Here, the native shape of the protein seems to be conserved. In contrast, the adsorption at the liquid/gas interface is mainly driven by hydrophobic effects, presumably by extending the hydrophobic regions of the amphipathic helices, and results in a conformational change of the protein during adsorption. However, the addition of differently charged membrane-forming lipids at the liquid/gas interface illustrates the ability of apoA1 to include lipids, resulting in a depletion of the lipids from the interface.

Factors affecting the physical stability (aggregation) of peptide therapeutics

The number of biological therapeutic agents in the clinic and development pipeline has increased dramatically over the last decade and the number will undoubtedly continue to increase in the coming years. Despite this fact, there are considerable challenges in the development, production and formulation of such biologics particularly with respect to their physical stabilities. There are many cases where self-association to form either amorphous aggregates or highly structured fibrillar species limits their use. Here, we review the numerous factors that influence the physical stability of peptides including both intrinsic and external factors, wherever possible illustrating these with examples that are of therapeutic interest. The effects of sequence, concentration, pH, net charge, excipients, chemical degradation and modification, surfaces and interfaces, and impurities are all discussed. In addition, the effects of physical parameters such as pressure, temperature, agitation and lyophilization are described. We provide an overview of the structures of aggregates formed, as well as our current knowledge of the mechanisms for their formation.

Femtosecond-Laser-Enhanced Amyloid Fibril Formation of Insulin

Femtosecond (fs)-laser-induced crystallization as a novel crystallization technique was proposed for the first time by our group, where the crystallization time can be significantly shortened under fs laser irradiation. Similarly, we have further extended our investigation to amyloid fibril formation, also known as a nucleation-dependence process. Here we demonstrate that the necessary time for amyloid fibril formation can be significantly shortened by fs laser irradiation, leading to favorable enhancement. The enhancement was confirmed by both spectral measurements and direct observations of amyloid fibrils. The thioflavin T fluorescence intensity of laser-irradiated solution increased earlier than that of the control solution, and such a difference was simultaneously revealed by ellipticity changes. At the same time before intensity saturation in fluorescence, the number of amyloid fibrils obtained under laser irradiation was generally more than that in the control solution. Besides, such an enhancement is correlated to the laser power threshold of cavitation bubbling. Possible mechanisms are proposed by referring to fs-laser-induced crystallization and ultrasonication-induced amyloid fibril formation.

Change of the isoelectric point of hemoglobin at the air/water interface probed by the orientational flip-flop of water molecules

Nonlinear vibrational spectroscopy reveals that the isoelectric point of proteins can largely change when the proteins are adsorbed at the air/water interface.

Insulin Aggregation at a Dynamic Solid-Liquid-Air Triple Interface

Therapeutic proteins are privileged in drug development because of their exquisite specificity, which is due to their three-dimensional conformation in solution. During their manufacture, storage, and delivery, interactions with material surfaces and air interfaces are known to affect their stability. The growing use of automated devices for handling and injection of therapeutics increases their exposure to protocols involving intermittent wetting, during which the solid-liquid and liquid-air interfaces meet at a triple contact line, which is often dynamic. Using a microfluidic setup, we analyze the effect of a moving triple interface on insulin aggregation in real time over a hydrophobic surface. We combine thioflavin T fluorescence and reflection interference microscopy to concomitantly monitor insulin aggregation and the morphology of the liquid as it dewets the surface. We demonstrate that insulin aggregates in the region of a moving triple interface and not in regions submitted to hydrodynamic shear stress alone, induced by the moving liquid. During dewetting, liquid droplets form on the surface anchored by adsorbed proteins, and the accumulation of amyloid aggregates is observed exclusively as fluorescent rings growing eccentrically around these droplets. The fluorescent rings expand until the entire channel surface sweeped by the triple interface is covered by amyloid fibers. On the basis of our experimental results, we propose a model describing the growth mechanism of insulin amyloid fibers at a moving triple contact line, where proteins adsorbed at a hydrophobic surface are exposed to the liquid-air interface.

In Situ Investigation of Peptide-Lipid Interaction Between PAP248-286 and Model Cell Membranes

Sum frequency generation vibrational spectroscopy (SFG) was utilized to investigate the interaction between PAP248-286 and the two lipid bilayer systems. The present study also provides spectroscopic evidence to confirm that, although PAP248-286 is unable to penetrate into the hydrophobic core of the lipid bilayers, it is capable of interacting more intimately with the fluid-phase POPG/POPC than with the gel-phase DPPG/DPPC lipid bilayer. The helical structure content of lipid-bound PAP248-286 was also observed to be high, in contrast to the results previously reported using nuclear magnetic resonance (NMR). Collectively, our SFG data suggest that lipid-bound PAP248-286 actually resembles its structure in 50 % 2,2,2-trifluoroethanol better than the structure when the peptide binds to SDS micelles. This present study questions the use of SDS micelles as the model membrane for NMR studies of PAP248-286 due to its protein denaturing activity.

Salt induced reduction of lysozyme adsorption at charged interfaces

A study of lysozyme adsorption below a behenic acid membrane and at the solid-liquid interface between aqueous lysozyme solution and a silicon wafer in the presence of sodium chloride is presented. The salt concentration was varied between 1 mmol L(-1) and 1000 mmol L(-1). X-ray reflectivity data show a clear dependence of the protein adsorption on the salt concentration. Increasing salt concentrations result in a decreased protein adsorption at the interface until a complete suppression at high concentrations is reached. This effect can be attributed to a reduced attractive electrostatic interaction between the positively charged proteins and negatively charged surfaces by charge screening. The measurements at the solid-liquid interfaces show a transition from unoriented order of lysozyme in the adsorbed film to an oriented order with the short protein axis perpendicular to the solid-liquid interface with rising salt concentration.