Importance of collision cross section measurements by ion mobility mass spectrometry in structural biology

The field of ion mobility mass spectrometry (IM‐MS) has developed rapidly in recent decades, with new fundamental advances underpinning innovative applications. This has been particularly noticeable in the field of biomacromolecular structure determination and structural biology, with pioneering studies revealing new structural insight for complex protein assemblies which control biological function. This perspective offers a review of recent developments in IM‐MS which have enabled expanding applications in protein structural biology, principally focusing on the quantitative measurement of collision cross sections and their interpretation to describe higher order protein structures.     

DIRECT‐ID: An automated method to identify and quantify conformational variations—application to β2‐adrenergic GPCR

The conformational dynamics of a macromolecule can be modulated by a number of factors, including changes in environment, ligand binding, and interactions with other macromolecules, among others. We present a method that quantifies the differences in macromolecular conformational dynamics and automatically extracts the structural features responsible for these changes. Given a set of molecular dynamics (MD) simulations of a macromolecule, the norms of the differences in covariance matrices are calculated for each pair of trajectories. A matrix of these norms thus quantifies the differences in conformational dynamics across the set of simulations. For each pair of trajectories, covariance difference matrices are parsed to extract structural elements that undergo changes in conformational properties. As a demonstration of its applicability to biomacromolecular systems, the method, referred to as DIRECT‐ID, was used to identify relevant ligand‐modulated structural variations in the β₂‐adrenergic (β₂AR) G‐protein coupled receptor. Micro‐second MD simulations of the β₂AR in an explicit lipid bilayer were run in the apo state and complexed with the ligands: BI‐167107 (agonist), epinephrine (agonist), salbutamol (long‐acting partial agonist), or carazolol (inverse agonist). Each ligand modulated the conformational dynamics of β₂AR differently and DIRECT‐ID analysis of the inverse‐agonist vs. agonist‐modulated β₂AR identified residues known through previous studies to selectively propagate deactivation/activation information, along with some previously unidentified ligand‐specific microswitches across the GPCR. This study demonstrates the utility of DIRECT‐ID to rapidly extract functionally relevant conformational dynamics information from extended MD simulations of large and complex macromolecular systems. © 2015 Wiley Periodicals, Inc.     

Detecting Counterion Dynamics in DNA–Protein Association

Due to a high density of negative charges on its surface, DNA condenses cations as counterions, forming the so‐called “ion atmosphere”. Although the release of counterions upon DNA–protein association has been postulated to have a major contribution to the binding thermodynamics, this release remains to be confirmed through a direct observation of the ions. Herein, we report the characterization of the ion atmosphere around DNA using NMR spectroscopy and directly detect the release of counterions upon DNA–protein association. NMR‐based diffusion data reveal the highly dynamic nature of counterions within the ion atmosphere around DNA. Counterion release is observed as an increase in the apparent ionic diffusion coefficient, which directly provides the number of counterions released upon DNA–protein association.     

Biomolecular hydration dynamics probed with 2D-IR spectroscopy: From dilute solution to a macromolecular crowd

Although it is well known that water is essential for biological function, it has been a challenge to determine how water behaves near biomacromolecular interfaces, and what role water plays in influencing the dynamics of the biochemical machinery. By adopting a vibrational labeling strategy coupled with ultrafast two-dimensional infrared (2D-IR) spectroscopy, it has recently become possible to study hydration dynamics, site specifically at the surface of proteins and model membranes. We review our recent progress in measuring hydration dynamics in contexts ranging from small-molecule solutes to biomacromolecules in dilute, viscous, and crowded environments.     

Photo‐Modulated Therapeutic Protein Release from a Hydrogel Depot Using Visible Light

The use of biomacromolecular therapeutics has revolutionized disease treatment, but frequent injections are required owing to their short half‐life in vivo. Thus there is a need for a drug delivery system that acts as a reservoir and releases the drug remotely “on demand”. Here we demonstrate a simple light‐triggered local drug delivery system through photo‐thermal interactions of polymer‐coated gold nanoparticles (AuNPs) inside an agarose hydrogel as therapeutic depot. Localized temperature increase induced by the visible light exposure caused reversible softening of the hydrogel matrix to release the pre‐loaded therapeutics. The release profile can be adjusted by AuNPs and agarose concentrations, light intensity and exposure time. Importantly, the biological activity of the released bevacizumab was highly retained. In this study we demonstrate the potential application of this facile AuNPs/hydrogel system for ocular therapeutics delivery through its versatility to release multiple biologics, compatibility to ocular cells and spatiotemporal control using visible light.     

Structural Transformation of Bovine Serum Albumin Induced by Dimethyl Sulfoxide and Probed by Fluorescence Correlation Spectroscopy and Additional Methods

Determining the structure of a protein and its transformation under different conditions is key to understanding its activity. The structural stability and activity of proteins in aqueous–organic solvent mixtures, which is an intriguing topic of research in biochemistry, is dependent on the nature of the protein and the properties of the medium. Herein, the effect of a commonly used cosolvent, dimethyl sulfoxide (DMSO), on the structure and conformational dynamics of bovine serum albumin (BSA) protein is studied by fluorescence correlation spectroscopy (FCS) measurements on fluorescein isothiocyanate (FITC)‐labeled BSA. The FCS study reveals a change of the hydrodynamic radius of BSA from 3.7 nm in the native state to 7.0 nm in the presence of 40 % DMSO, which suggests complete unfolding of the protein under these conditions. Fluorescence self‐quenching of FITC has been exploited to understand the conformational dynamics of BSA. The time constant of the conformational dynamics of BSA is found to change from 35 μs in its native state to 50 μs as the protein unfolds with increasing DMSO concentration. The FCS results are corroborated by the near‐UV circular dichroism spectra of the protein, which suggest a loss of its tertiary structure with increasing concentration of DMSO. The intrinsic fluorescence of BSA and the fluorescence response of 1‐anilinonaphthalene‐8‐sulfonic acid, used as a probe molecule, provide information that is consistent with the FCS measurements, except that aggregation of BSA is observed in the presence of 40 % DMSO in the ensemble measurements.     

Dynamics of cyclodimerization and viscoelasticity of photo‐crosslinkable PVA

We investigated the interfacial properties of poly(vinyl alcohol) carrying UV‐crosslinkable pendant quaternized stilbazole (styrylpyridinium), PVA‐SbQ. The extent and dynamics of PVA‐SbQ cyclodimerization reactions and crosslinking induced by UV irradiation were monitored in situ and in real time by quartz crystal microgravimetry (QCM). Sensograms reflecting time‐dependent changes in density and viscoelasticity of crosslinking films followed a Boltzmann sigmoidal model, depending on precursor film composition and irradiation power. The shifts in QCM frequency and energy dissipation upon PVA‐SbQ cyclodimerization correlated with three photo‐crosslinking phases involving soft‐to‐rigid transitions, namely, induction (initiation), main crosslinking (interaction), and termination. PVA‐SbQ films crosslinked to different degree were used as protein carriers and a slower release profile was determined for the films that underwent more extensive crosslinking. Overall, this study demonstrates for the first time the dynamics of PVA‐SbQ crosslinking and its impact in system viscoelasticity and protein release. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 345–355     

Novel drug‐eluting soy‐protein structures for wound healing applications

Naturally derived materials are becoming widely used in the biomedical field. Soy protein has advantages over the various types of natural proteins employed for biomedical applications due to its low price, nonanimal origin, and relatively long storage time and stability. In the current study, novel drug‐eluting soy‐protein films for wound healing applications were developed and studied. The films were prepared using the solvent casting technique. The analgesic drug bupivacaine and two types of wide range antibiotics (gentamicin and clindamycin) were incorporated into the soy‐protein films. The effect of drug incorporation and plasticizers content on the films' mechanical properties, drug release profiles, and cell viability was studied. Drug incorporation had a softening effect of the films, lowering mechanical strength and increasing ductility. Release profiles of bupivacaine and clindamycin exhibited high burst release of 80% to 90% of encapsulated drug within 6 hours, followed by continuous release in a decreasing rate for a period of 2 to 4 days. Gentamicin release was prolonged, probably due to interaction between the gentamicin and the polymer chains. Hybrid soy‐protein/poly (Dl‐lactic‐co‐glycolic acid) (PDLGA) microspheres structure showed potential for long and sustained release of bupivacaine. Films with no drugs and films loaded with gentamicin were found to be noncytotoxic for human fibroblasts, while bupivacaine and clindamycin were found to have some effect on cell growth. In conclusion, our new drug‐loaded soy‐protein films combine good mechanical properties and biocompatibility, with desired drug release profiles, and can therefore be potentially very useful as burn and ulcer dressings.     

Site‐Resolved Backbone and Side‐Chain Intermediate Dynamics in a Carbohydrate‐Binding Module Protein Studied by Magic‐Angle Spinning NMR Spectroscopy

Magic‐angle spinning solid‐state NMR spectroscopy has been applied to study the dynamics of CBM3b–Cbh9A from Clostridium thermocellum (ctCBM3b), a cellulose binding module protein. This 146‐residue protein has a nine‐stranded β‐sandwich fold, in which 35 % of the residues are in the β‐sheet and the remainder are composed of loops and turns. Dynamically averaged ¹H‐¹³C dipolar coupling order parameters were extracted in a site‐specific manner by using a pseudo‐three‐dimensional constant‐time recoupled separated‐local‐field experiment (dipolar‐chemical shift correlation experiment; DIPSHIFT). The backbone‐Cα and Cβ order parameters indicate that the majority of the protein, including turns, is rigid despite having a high content of loops; this suggests that restricted motions of the turns stabilize the loops and create a rigid structure. Water molecules, located in the crystalline interface between protein units, induce an increased dynamics of the interface residues thereby lubricating crystal water‐mediated contacts, whereas other crystal contacts remain rigid.     

Identifying Protein Conformational Dynamics Using Spin‐label ESR

Spin‐label electron spin resonance (ESR) has emerged as a powerful tool to characterize protein dynamics. One recent advance is the development of ESR for resolving dynamical components that occur or coexist during a biological process. It has been applied to study the complex structural and dynamical aspects of membranes and proteins, such as conformational changes in protein during translocation from cytosol to membrane, conformational exchange between equilibria in response to protein‐protein and protein‐ligand interactions in either soluble or membrane environments, protein oligomerization, and temperature‐ or hydration‐dependent protein dynamics. As these topics are challenging but urgent for understanding the function of a protein on the molecular level, the newly developed ESR methods to capture individual dynamical components, even in low‐populated states, have become a great complement to other existing biophysical tools.     

Cell‐Permeant and Photocleavable Chemical Inducer of Dimerization

Chemical inducers of dimerization (CIDs) have been developed to orchestrate protein dimerization and translocation. Here we present a novel photocleavable HaloTag‐ and SNAP‐tag‐reactive CID (MeNV‐HaXS) with excellent selectivity and intracellular reactivity. Excitation at 360 nm cleaves the methyl‐6‐nitroveratryl core of MeNV‐HaXS. MeNV‐HaXS covalently links HaloTag‐ and SNAP‐tag fusion proteins, and enables targeting of selected membranes and intracellular organelles. MeNV‐HaXS‐mediated translocation has been validated for plasma membrane, late endosomes, lysosomes, Golgi, mitochondria, and the actin cytoskeleton. Photocleavage of MeNV‐HaXS liberates target proteins and provides access to optical manipulation of protein relocation with high spatiotemporal and subcellular precision. MeNV‐HaXS supports kinetic studies of protein dynamics and the manipulation of subcellular enzyme activities, which is exemplified for Golgi‐targeted cargo and the assessment of nuclear import kinetics.     

Implicit treatment of solvent dispersion forces in protein simulations

A model is proposed for the evaluation of dispersive forces in a continuum solvent representation for use in large‐scale computer simulations. The model captures the short‐ and long‐range effects of water‐exclusion in conditions of partial and anisotropic hydration. The model introduces three parameters, one of which represents the degree of hydration (water occupancy) at any point in the system, which depends on the solute conformation, and two that represent the strength of water–water and water–solute dispersive interactions. The model is optimized for proteins, using hydration data of a suboptimally hydrated binding site and results from dynamics simulations in explicit water. The model is applied to a series of aliphatic‐alcohol/protein complexes and a set of binary and ternary complexes of various sizes. Implications for weak and ultra‐weak protein‐protein association and for simulation in crowded media are discussed. Published 2014. This article is a U.S. Government work and is in the public domain in the USA     

Collisional and Coulombic Unfolding of Gas‐Phase Proteins: High Correlation to Their Domain Structures in Solution

The three‐dimensional structures adopted by proteins are predicated by their many biological functions. Mass spectrometry has played a rapidly expanding role in protein structure discovery, enabling the generation of models for both proteins and their higher‐order assemblies. While important coursed‐grained insights have been generated, relatively few examples exist where mass spectrometry has been successfully applied to the characterization of protein tertiary structure. Here, we demonstrate that gas‐phase unfolding can be used to determine the number of autonomously folded domains within monomeric proteins. Our ion mobility‐mass spectrometry data highlight a strong, positive correlation between the number of protein unfolding transitions observed in the gas phase and the number of known domains within a group of sixteen proteins ranging from 8–78 kDa. This correlation and its potential uses for structural biology is discussed.     

Future directions of structural mass spectrometry using hydroxyl radical footprinting

Hydroxyl radical protein footprinting coupled to mass spectrometry has been developed over the last decade and has matured to a powerful method for analyzing protein structure and dynamics. It has been successfully applied in the analysis of protein structure, protein folding, protein dynamics, and protein–protein and protein–DNA interactions. Using synchrotron radiolysis, exposure of proteins to a ‘white’ X‐ray beam for milliseconds provides sufficient oxidative modification to surface amino acid side chains, which can be easily detected and quantified by mass spectrometry. Thus, conformational changes in proteins or protein complexes can be examined using a time‐resolved approach, which would be a valuable method for the study of macromolecular dynamics. In this review, we describe a new application of hydroxyl radical protein footprinting to probe the time evolution of the calcium‐dependent conformational changes of gelsolin on the millisecond timescale. The data suggest a cooperative transition as multiple sites in different molecular subdomains have similar rates of conformational change. These findings demonstrate that time‐resolved protein footprinting is suitable for studies of protein dynamics that occur over periods ranging from milliseconds to seconds. In this review, we also show how the structural resolution and sensitivity of the technology can be improved as well. The hydroxyl radical varies in its reactivity to different side chains by over two orders of magnitude, thus oxidation of amino acid side chains of lower reactivity are more rarely observed in such experiments. Here we demonstrate that the selected reaction monitoring (SRM)‐based method can be utilized for quantification of oxidized species, improving the signal‐to‐noise ratio. This expansion of the set of oxidized residues of lower reactivity will improve the overall structural resolution of the technique. This approach is also suggested as a basis for developing hypothesis‐driven structural mass spectrometry experiments. Copyright © 2010 John Wiley & Sons, Ltd.     

Human serum albumin in electrospun PCL fibers: structure,release, and exposure on fiber surface

Human serum albumin (HSA) introduced to the fibers produced by electrospinning from HSA and polycaprolactone (PCL) solutions in hexafluoroisopropanol has been studied in terms of its structure, release from the fibers, stability of interaction with basic polymer, accessibility for protease attack, and cellular receptors, as well as dependence of the studied parameters on the protein concentration in fibers. A limited part of the protein leaves the fibers right after soaking with water, whereas the remaining protein stays tightly bound to fibers for a long time because protein nanoparticles are tightly integrated with PCL, as shown by small‐angle X‐ray scattering. As has been demonstrated, the proteins leave the fibers in complexes with PCL. X‐ray photoelectron spectroscopy demonstrates that the protein concentration on the fiber surface is higher than the concentration in electrospinning solution. The surface‐exposed protein is recognized by cell receptors and is partially hydrolyzed by proteinase K. The data on pulse protein release, presence of PCL in the protein released from matrixes, overrepresentation of the protein on the fiber surface, and tight interaction of protein with PCL may be useful for rational design of electrospun scaffolds intended for drug delivery and tissue engineering. Copyright © 2016 John Wiley & Sons, Ltd.     

Flexible protein‐ligand docking using the Fleksy protocol

Considering protein plasticity is important in accurately predicting the three‐dimensional geometry of protein‐ligand complexes. Here, we present the first public release of our flexible docking tool Fleksy, which is able to consider both ligand and protein flexibility in the docking process. We describe the workflow and different features of the software and present its performance on two cross‐docking benchmark datasets. © 2012 Wiley Periodicals, Inc.     

Polymeric Lids for Microcontainers for Oral Protein Delivery

Oral delivery of proteins and peptides is one of the main challenges in pharmaceutical drug development. Microdevices have the possibility to protect the therapeutics until release is desired, avoiding losses by degradation. One type of microdevice is polymeric microcontainers. In this study, lysozyme is chosen as model protein and loaded into microcontainers with the permeation enhancer sodium decanoate (C10). The loaded microcontainers are sealed and functionalized by applying polymeric lids onto the cavity of the devices. The first lid is poly(lactic‐co‐glycolic) acid (PLGA) and on top of this either polyethylene glycol (PEG) or chitosan is applied (PLGA+PEG or PLGA+chitosan, respectively). The functionalization is evaluated in vitro for morphology, drug release, and mucoadhesive properties. These are coupled with in vitro and ex vivo studies using Caco‐2 cells, Caco‐2/HT29‐MTX‐E12 co‐cultures, and porcine intestinal tissue. PLGA+chitosan shows slower release compared to PLGA+PEG or only PLGA in buffer and the transport of lysozyme across cell cultures is not enhanced compared to the bulk powder. Microcontainers coated with chitosan or PEG demonstrate a three times stronger adhesion during ex vivo mucoadhesion studies compared to samples without coatings. Altogether, functionalized microcontainers with mucoadhesive properties and tunable release for oral protein delivery are developed and characterized.     

Computational study of ligand binding in lipid transfer proteins: Structures,interfaces, and free energies of protein‐lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein‐ligand interactions. We present here a computational study of protein‐ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries in molecular dynamics calculations, we computed Poisson‐Boltzmann electrostatic potentials, solvation energies, properties of the protein‐ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein‐lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity. © 2012 Wiley Periodicals, Inc.     

Unveiling the Role of DJ‐1 Protein in Vesicular Storage and Release of Catecholamine with Nano/Micro‐Tip Electrodes

DJ‐1 protein deficiency caused by PARK7 gene mutation has been suggested to closely relate to Parkinson's disease (PD), mainly through the attenuation D2 dopamine receptor activity in mice; however, whether or how it affects the vesicular storage and exocytosis of neurochemicals remains unclear. By using electrochemical methods at a single vesicle/cell level with nano/micro‐tip electrodes, we for the first time find that DJ‐1 protein deficiency caused by PARK7 gene knockout (KO) in mice has little effect on vesicular catecholamine content but significantly prolongs the exocytotic events, especially the closing time of exocytotic fusion pores. Further studies suggest the inhibition of α‐synuclein aggregation by DJ‐1 protein might be one way that DJ‐1 protein acts on neurotransmission. This finding offers the first direct link between DJ‐1 protein deficiency and vesicular chemical storage and release of chemicals, providing a new chemical insight into the pathology of PD caused by PARK7 gene mutation.