How to run molecular dynamics simulations on electrospray droplets and gas phase proteins: Basic guidelines and selected applications

High-Performance Molecular Dynamics Simulations for Native Mass Spectrometry of Large Protein Complexes with the Fast Multipole Method

Native mass spectrometry (MS) is widely employed to study the structures and assemblies of proteins ranging from small monomers to megadalton complexes. Molecular dynamics (MD) simulation is a useful complement as it provides the spatial detail that native MS cannot offer. However, MD simulations performed in the gas phase have suffered from rapidly increasing computational costs with the system size. The primary bottleneck is the calculation of electrostatic forces, which are effective over long distances and must be explicitly computed for each atom pair, precluding efficient use of methods traditionally used to accelerate condensed-phase simulations. As a result, MD simulations have been unable to match the capacity of MS in probing large multimeric protein complexes. Here, we apply the fast multipole method (FMM) for computing the electrostatic forces, recently implemented by Kohnke et al. (J. Chem. Theory Comput., 2020, 16, 6938-6949), showing that it significantly enhances the performance of gas-phase simulations of large proteins. We assess how to achieve adequate accuracy and optimal performance with FMM, finding that it expands the accessible size range and time scales dramatically. Additionally, we simulate a 460 kDa ferritin complex over microsecond time scales, alongside complementary ion mobility (IM)-MS experiments, uncovering conformational changes that are not apparent from the IM-MS data alone.

Dynamics of collisions and uptake of alcohol molecules with hydrated nitric acid clusters

We investigate the collisions of different alcohol molecules with hydrated nitric acid clusters using a molecular beam experiment and molecular dynamics simulations. The uptake cross sections σp for the molecules evaluated from the experiment are in excellent agreement with the simulations. This suggests that (i) the nontrivial assumptions implemented in the evaluation procedure of the experimental data are valid, and (ii) the simulations describe correctly the major processes in the molecule-cluster collisions. We observe that σp decreases with the increasing alkyl chain length of the alcohol, and also with the branching of the molecules that have the same mass but different structures. These systematic trends can be rationalized based on the accessibility of the hydrophilic OH group, which decreases with the increasing chain length and steric hindrance. The observed trends and their interpretation differ significantly from the simple model of hard-sphere collisions. The obtained data shall be beneficial not only for the fundamental understanding of the molecule-cluster collisions, but also in the modelling of atmospheric new-particle formation and aerosol growth.

Electrospray ionization tandem mass spectrometry of 4-aryl-3,4-dihydrocoumarins

We have investigated the gas-phase fragmentation reactions of 11 synthetic 4-aryl-3,4-dihydrocoumarins by electrospray ionization tandem mass spectrometry (ESI-MS/MS) on a quadrupole-time-of flight (Q-TOF) hybrid mass spectrometer. We have also estimated thermochemical data for the protonated coumarins (precursor ion A) and product ion structures by computational chemistry at a B3LYP level of theory to establish the ion structures and to rationalize the fragmentation pathways. The most abundant ions in the product ion spectra of coumarins 1-11 resulted from C8H8O2, CO2, C4H4O3, C8H10O3, C8H8O2, and CH3OH eliminations through retro-Diels-Alder (RDA) reactions, remote hydrogen rearrangements (β-eliminations), and β-lactone ring contraction. Although the investigated coumarins shared most of the fragmentation pathways, formation of a benzylic product ion and its corresponding tropylium ion was diagnostic of the substituents at ring C. The thermochemical data revealed that the nature and position of the substituents at ring C played a key role in the formation of this product ion and determined its relative intensity in the product ion spectrum. The results of this study contribute to knowledge of the gas-phase ion chemistry of this important class of organic compounds.

MD Simulations of Peptide-Containing Electrospray Droplets: Effects of Parameter Settings on the Predicted Mechanisms of Gas Phase Ion Formation

Electrospray ionization (ESI) mass spectrometry is widely used for interrogating peptides, proteins, and other biomolecular analytes. A growing number of laboratories use molecular dynamics (MD) simulations for uncovering ESI mechanisms by modeling the behavior of highly charged nanodroplets. The outcome of any MD simulation depends on certain assumptions and parameter settings, and it is desirable to optimize these factors by benchmarking computational data against experiments. Unfortunately, benchmarking of ESI simulations is difficult because experimentally generated gaseous ions do not generally retain any features that would reveal their formation pathway [e.g., the charged residue mechanism (CRM) or the ion evaporation mechanism (IEM)]. Here, we tackle this problem by examining the effects of various MD settings on the ESI behavior of the 9-residue peptide bradykinin in acidic aqueous droplets. Several parameters were found to significantly affect the kinetic competition between peptide IEM and CRM. By systematically probing the droplet behavior, we uncovered problems associated with certain settings, including peptide/solvent temperature imbalances, unexpected peptide deceleration during IEM, and a dependence of the ESI mechanism on the water model. We also noted different simulation outcomes for different force fields. On the basis of comprehensive tests, we propose a set of "best practice" parameter settings for MD simulations of ESI droplets. The strategies used here should be transferable to other types of droplet simulations, paving the way toward a more solid understanding of ESI mechanisms.

Biomolecular dynamics with machine-learned quantum-mechanical force fields trained on diverse chemical fragments

The GEMS method enables molecular dynamics simulations of large heterogeneous systems at ab initio quality.

Interactions of ferulic acid and ferulic acid methyl ester with endogenous proteins: Determination using the multi-methods

Ferulic acid (FA) and ferulic acid methyl ester (FAM) are important phenolic compounds in Baijiu. In this study, the interaction of FA and FAM with human serum albumin (HSA) and lysozyme (LZM) was investigated using multispectral methods and molecular dynamics simulation. FA and FAM could interact with HSA and LZM, changing the conformation and hydrophilicity of the protein. The quenching mechanisms of FA-HSA, FA-LZM, FAM-HSA, and FAM-LZM were all static-quenching. In the FA-HSA, FAM-HSA, and FA-LZM systems, the interaction forces were mainly hydrophobic interactions and hydrogen bonding. In the FAM-LZM system, the interaction forces were mainly hydrophobic interactions, hydrogen bonding, and van der Waals force. Common metal ions such as K+, Ca2+, Cu2+, Mg2+, and Mn2+ could affect the binding ability of FA and FAM to HSA and LZM. Moreover, FA and FAM could increase the stability of HSA and LZM, and the protein bound to FA/FAM was more stable than the free protein. FA and FAM had varying degrees of impact on the physiological activities of HSA and LZM. This study provides relevant information on the interactions and metabolic mechanisms of FA and its derivatives with endogenous proteins.

Evidence of H/D Exchange within Metal-Adducted Carbohydrates after Ion/Ion-Dissociation Reactions

Tandem mass spectrometry (MS/MS) using fragmentation has become one of the most effective methods for gaining sequence and structural information on biomolecules. Ion/ion reactions are competitive reactions, where either proton transfer (PT) or electron transfer (ET) can occur from interactions between multiply charged cations and singly charged anions. Utilizing ion/ion reactions with fluoranthene has offered a unique method of fragment formation for the structural elucidation of biomolecules. Fluoranthene is considered an ideal anion reagent because it selectively causes electron-transfer dissociation (ETD) and minimizes PT when interacting with peptides. However, limited investigations have sought to understand how fluoranthene─the primary, commercially available anion reagent─interacts with other biomolecules. Here, we apply deuterium labeling to investigate ion/ion reaction mechanisms between fluoranthene and divalent, metal-adducted carbohydrates (Ca2+, Mg2+, Co2+, and Ni2+). Deuterium labeling of carbohydrates allowed us to observe evidence of hydrogen/deuterium exchange (HDX) occurring after ion/ion dissociation reactions. The extent of deuterium loss is dependent on several factors, including the physical properties of the metal ion and the fragment structure. Based on the deuterium labeling data, we have proposed ETD, PTD, and intermolecular PT─also described as HDX─mechanisms. This research provides a fundamental perspective of ion/ion and ion/molecule reaction mechanisms and illustrates properties that impact ion/ion and ion/molecule reactions for carbohydrates. Together, this could improve the capability to distinguish complex and heterogeneous biomolecules, such as carbohydrates.

Predicting Preferences for Adduct Formation in Electrospray Ionization: The Case Study of Succinic Acid

A simple theoretical approach is developed that can be used to predict the preference of ion adduct formation (with alkali Li⁺, Na⁺, K⁺ and alkaline earth Ca²⁺, Mg²⁺ metals) in electrospray ionization mass spectrometry (ESI-MS) of succinic acid, associated with several protonation/deprotonation equilibria. The applied strategy consists of using a vacuum environment as well as both implicit and explicit solvation of reactive sites and density functional theory as the method of choice. These distinct levels of theory mimic the smooth transition between the condensed environment and free ion in the gas phase. Good correlation between the Gibbs free energies for protonation/adduct formation processes with peak observation in the obtained mass spectra provide insight into the physical basis behind adduct preference and selectivity. This signifies the relationship between microscopic interactions, ionization efficiency, and types of ions that reach the detector.

Understanding of protomers/deprotomers by combining mass spectrometry and computation

Multifunctional compounds may form different prototropic isomers under different conditions, which are known as protomers/deprotomers. In biological systems, these protomer/deprotomer isomers affect the interaction modes and conformational landscape between compounds and enzymes and thus present different biological activities. Study on protomers/deprotomers is essentially the study on the acidity/basicity of each intramolecular functional group and its effect on molecular structure. In recent years, the combination of mass spectrometry (MS) and computational chemistry has been proven to be a powerful and effective means to study prototropic isomers. MS-based technologies are developed to discriminate and characterize protomers/deprotomers to provide structural information and monitor transformations, showing great superiority than other experimental methods. Computational chemistry is used to predict the thermodynamic stability of protomers/deprotomers, provide the simulated MS/MS spectra, infrared spectra, and calculate collision cross-section values. By comparing the theoretical data with the corresponding experimental results, the researchers can not only determine the protomer/deprotomer structure, but also investigate the structure-activity relationship in a given system. This review covers various MS methods and theoretical calculations and their devotion to isomer discrimination, structure identification, conformational transformation, and phase transition investigation of protomers/deprotomers.

Release of nanodiscs from charged nano-droplets in the electrospray ionization revealed by molecular dynamics simulations

Electrospray ionization (ESI) is essential for application of mass spectrometry in biological systems, as it prevents the analyte being split into fragments. However, due to lack of a clear understanding of the mechanism of ESI, the interpretation of mass spectra is often ambiguous. This is a particular challenge for complex biological systems. Here, we focus on systems that include nanodiscs as membrane environment, which are essential for membrane proteins. We performed microsecond atomistic molecular dynamics simulations to study the release of nanodiscs from highly charged nano-droplets into the gas phase, the late stage of ESI. We observed two distinct major scenarios, highlighting the diversity of morphologies of gaseous product ions. Our simulations are in reasonable agreement with experimental results. Our work provides a detailed atomistic view of the ESI process of a heterogeneous system (lipid nanodisc), which may give insights into the interpretation of mass spectra of all lipid-protein systems.

Native Electrospray Ionization of Multi-Domain Proteins via a Bead Ejection Mechanism

Native ion mobility mass spectrometry is potentially useful for the biophysical characterization of proteins, as the electrospray charge state distribution and the collision cross section distribution depend on their solution conformation. We examine here the charging and gas-phase conformation of multi-domain therapeutic proteins comprising globular domains tethered by disordered linkers. The charge and collision cross section distributions are multimodal, suggesting several conformations in solution, as confirmed by solution hydrogen/deuterium exchange. The most intriguing question is the ionization mechanism of these structures: a fraction of the population does not follow the charged residue mechanism but cannot ionize by pure chain ejection either. We deduce that a hybrid mechanism is possible, wherein globular domains are ejected one at a time from a parent droplet. The charge vs solvent accessible surface area correlations of denatured and intrinsically disordered proteins are also compatible with this "bead ejection mechanism", which we propose as a general tenet of biomolecule electrospray.

Evaluation and optimization of the influence of silver cluster ions on the MALDI-TOF-MS analysis of polystyrene nanoplastic polymers

In the analysis of polystyrene nanoplastics (PSNs), a nonpolar polymer (NP), using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), silver salts were used as cationization reagents and simultaneously brought the potential problems of silver clusters that interfered with the PSN signal of MS. To detect PSNs, silver trifluoroacetate (AgTFA) and silver nitrate (AgNO₃) were mixed with five polar matrices, namely 2-(4-hydroxyphenylazo) benzoic acid (HABA), dithranol (DI), sinapic acid (SA), trans-3-indoleacrylic acid (IAA), and 2,5-dihydroxybenzoic acid (DHB), and three nonpolar matrices, namely pyrene (PRN), anthracene (ATH) and acenaphthene (ACTH). The results showed that silver salt cluster ions were detected in the range of m/z 1000-4000. Five polar matrices with silver salts produced silver clusters, which interfered with the signals in the mass spectrum of PSNs, but the combination of these matrices with copper II chloride (CuCl₂) salt did not produce copper-related clusters. However, the use of nonpolar matrices such as PRN, ATH or ACTH significantly decreased the signals of silver salt cluster ions, and this alteration of matrix types is considered a promising optimization approach for silver cluster ions. The nonpolar matrix conditions were optimized without producing silver cluster ions and the optimal detection conditions were found to be under nonpolar matrices (e.g., pyrene) with silver salts (e.g., AgTFA). The results suggest that when polar matrices, such as HABA, DI, SA, IAA, and DHB, are combined with silver salts in MALDI-TOF-MS analysis, silver-related clusters are detected in the range of m/z 1000-4000. Inhibition of the production of silver cluster ions can be achieved by the use of a nonpolar matrix (e.g., PRN) or polar matrix (e.g., DHB) with copper salts.

Investigation of Charge-State-Dependent Compaction of Protein Ions with Native Ion Mobility-Mass Spectrometry and Theory

The precise relationship between native gas-phase protein ion structure, charge, desolvation, and activation remains elusive. Much evidence supports the Charge Residue Model for native protein ions formed by electrospray ionization, but scaling laws derived from it relate only to overall ion size. Closer examination of drift tube CCSs across individual native protein ion charge state distributions (CSDs) reveals deviations from global trends. To investigate whether this is due to structure variation across CSDs or contributions of long-range charge-dipole interactions, we performed in vacuo force field molecular dynamics (MD) simulations of multiple charge conformers of three proteins representing a variety of physical and structural features: β-lactoglobulin, concanavalin A, and glutamate dehydrogenase. Results from these simulated ions indicate subtle structure variation across their native CSDs, although effects of these structural differences and long-range charge-dependent interactions on CCS are small. The structure and CCS of smaller proteins may be more sensitive to charge due to their low surface-to-volume ratios and reduced capacity to compact. Secondary and higher order structure from condensed-phase structures is largely retained in these simulations, supporting the use of the term "native-like" to describe results from native ion mobility-mass spectrometry experiments, although, notably, the most compact structure can be the most different from the condensed-phase structure. Collapse of surface side chains to self-solvate through formation of new hydrogen bonds is a major feature of gas-phase compaction and likely occurs during the desolvation process. Results from these MD simulations provide new insight into the relationship of gas-phase protein ion structure, charge, and CCS.

Suppression of Protein Structural Perturbations in Native Electrospray Ionization during the Final Evaporation Stages Revealed by Molecular Dynamics Simulations

Native electrospray ionization was known to preserve the protein structure in solution, which overcame the uncontrollable acidification of droplets during transfer from solution into the gas phase in conventional electrospray ionization. However, detailed experimental studies on when and how could native electrospray ionization minimize structural perturbations remain quite unclear. Herein, we conducted molecular dynamics simulations to investigate the protein structure evolution during electrospray ionization. At a neutral droplet pH, the protein structure in solution could be retained after evaporation, which was in accordance with previous reports. As the droplet pH deviated from neutral, we have found that the compact protein structure would not unfold until the last 10 ns prior to the final desolvation, which demonstrated that the role of native electrospray ionization in preserving the protein structure was mainly reflected on the final evaporation stages. The present study might provide new insights into studying the microscopic biomolecular events occurring during the liquid-gas interface transition and their influence on solution-structure retention.

Formation of Carbohydrate-Metal Adducts from Solvent Mixtures during Electrospray: A Molecular Dynamics and ESI-MS Study

Electrospray ionization (ESI) is frequently used to produce gas-phase ions for mass spectrometry (MS)-based techniques. The composition of solvents used in ESI-MS is often manipulated to enhance analyte ionization, including for carbohydrates. Moreover, to characterize analyte structures, ESI has been coupled to hydrogen/deuterium exchange, ion mobility, and tandem MS. Therefore, it is important to understand how solvent composition affects the structure of carbohydrates during and after ESI. In this work, we use molecular dynamics to simulate the desolvation of ESI droplets containing a model carbohydrate and observe the formation of carbohydrate adducts with metal ions. Molecular-level details on the effects of formulating mixtures of water, methanol, and acetonitrile to achieve enhanced ionization are presented. We complement our simulations with ESI-MS experiments. We report that when sprayed from aqueous mixtures containing volatile solvents, carbohydrates ionize to form metal-ion adducts rapidly due to rapid solvent evaporation rather than changes in the ionization mechanism. We find that when sprayed from solvent mixtures, carbohydrates are primarily solvated by water due to the migration of more volatile solvents to the surface of the droplet. Ultimately, the structure of the carbohydrate varies depending on its solvent environment, as inter- and intramolecular interactions are affected. We propose that solvents with 25% or more water may be used to enhance the ionization of carbohydrates with minimal effect on the structure during and after ESI.

SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic

Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), a large number of mutations in its genome have been reported. Some of the mutations occur in noncoding regions without affecting the pathobiology of the virus, while mutations in coding regions are significant. One of the regions where a mutation can occur, affecting the function of the virus is at the receptor‐binding domain (RBD) of the spike protein. RBD interacts with angiotensin‐converting enzyme 2 (ACE2) and facilitates the entry of the virus into the host cells. There is a lot of focus on RBD mutations, especially the displacement of N501Y which is observed in the UK/Kent, South Africa, and Brazilian lineages of SARS‐CoV‐2. Our group utilizes computational biology approaches such as immunoinformatics, protein–protein interaction analysis, molecular dynamics, free energy computation, and tertiary structure analysis to disclose the consequences of N501Y mutation at the molecular level. Surprisingly, we discovered that this mutation reduces the immunogenicity of the spike protein; also, displacement of Asn with Tyr reduces protein compactness and significantly increases the stability of the spike protein and its affinity to ACE2. Moreover, following the N501Y mutation secondary structure and folding of the spike protein changed dramatically.

p-Aminobenzoic acid protonation dynamics in an evaporating droplet by ab initio molecular dynamics

Protonation equilibria are known to vary from the bulk to microdroplet conditions, which could induce many chemical and physical phenomena. Protonated p-aminobenzoic acid (PABA + H⁺) can be considered a model for probing the protonation dynamics in an evaporating droplet, as its protonation equilibrium is highly dependent on the formation conditions from solution via atmospheric pressure ionization sources. Experiments using diverse experimental techniques have shown that protic solvents allow formation of the O-protomer (PABA protonated in the carboxylic acid group) stable in the gas phase, while aprotic solvents yield the N-protomer (protonated in the amino group) that is the most stable protomer in solution. In this work, we explore the protonation equilibrium of PABA solvated by different numbers of water molecules (n = 0 to 32) using ab initio molecular dynamics. For n = 8-32, the protonation is either at the NH₂ group or in the solvent network. The solvent network interacts with the carboxylic acid group, but there is no complete proton transfer to form the O-protomer. For smaller clusters, however, solvent-mediated proton transfers to the carboxylic acid were observed, both via the Grotthuss mechanism and the vehicle or shuttle mechanism (for n = 1 and 2). Thermodynamic considerations allowed a description of the origins of the kinetic trapping effect, which explains the observation of the solution structure in the gas phase. This effect likely occurs in the final evaporation steps, which are outside the droplet size range covered by previous classical molecular dynamics simulations of charged droplets. These results may be considered relevant in determining the nature of the species observed in the ubiquitous ESI based mass spectrometry analysis, and in general for droplet chemistry, explaining how protonation equilibria are drastically changed from bulk to microdroplet conditions.

Reaction Monitoring and Structural Characterisation of Coordination Driven Self-Assembled Systems by Ion Mobility-Mass Spectrometry

Nature creates exquisite molecular assemblies, required for the molecular-level functions of life, via self-assembly. Understanding and harnessing these complex processes presents an immense opportunity for the design and fabrication of advanced functional materials. However, the significant industrial potential of self-assembly to fabricate highly functional materials is hampered by a lack of knowledge of critical reaction intermediates, mechanisms, and kinetics. As we move beyond the covalent synthetic regime, into the domain of non-covalent interactions occupied by self-assembly, harnessing and embracing complexity is a must, and non-targeted analyses of dynamic systems are becoming increasingly important. Coordination driven self-assembly is an important subtype of self-assembly that presents several wicked analytical challenges. These challenges are "wicked" due the very complexity desired confounding the analysis of products, intermediates, and pathways, therefore limiting reaction optimisation, tuning, and ultimately, utility. Ion Mobility-Mass Spectrometry solves many of the most challenging analytical problems in separating and analysing the structure of both simple and complex species formed via coordination driven self-assembly. Thus, due to the emerging importance of ion mobility mass spectrometry as an analytical technique tackling complex systems, this review highlights exciting recent applications. These include equilibrium monitoring, structural and dynamic analysis of previously analytically inaccessible complex interlinked structures and the process of self-sorting. The vast and largely untapped potential of ion mobility mass spectrometry to coordination driven self-assembly is yet to be fully realised. Therefore, we also propose where current analytical approaches can be built upon to allow for greater insight into the complexity and structural dynamics involved in self-assembly.

Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors

The metabotropic glutamate receptors (mGluRs) form a family of neuromodulatory G-protein-coupled receptors that contain both a seven-helix transmembrane domain (TMD) and a large extracellular ligand-binding domain (LBD) which enables stable dimerization. Although numerous studies have revealed variability across subtypes in the initial activation steps at the level of LBD dimers, an understanding of inter-TMD interaction and rearrangement remains limited. Here, we use a combination of single molecule fluorescence, molecular dynamics, functional assays, and conformational sensors to reveal that distinct TMD assembly properties drive differences between mGluR subtypes. We uncover a variable region within transmembrane helix 4 (TM4) that contributes to homo- and heterodimerization in a subtype-specific manner and tunes orthosteric, allosteric, and basal activation. We also confirm a critical role for a conserved inter-TM6 interface in stabilizing the active state during orthosteric or allosteric activation. Together this study shows that inter-TMD assembly and dynamic rearrangement drive mGluR function with distinct properties between subtypes.

Interrogating the Quaternary Structure of Noncanonical Hemoglobin Complexes by Electrospray Mass Spectrometry and Collision-Induced Dissociation

Various activation methods are available for the fragmentation of gaseous protein complexes produced by electrospray ionization (ESI). Such experiments can potentially yield insights into quaternary structure. Collision-induced dissociation (CID) is the most widely used fragmentation technique. Unfortunately, CID of protein complexes is dominated by the ejection of highly charged monomers, a process that does not yield any structural insights. Using hemoglobin (Hb) as a model system, this work examines under what conditions CID generates structurally informative subcomplexes. Native ESI mainly produced tetrameric Hb ions. In addition, "noncanonical" hexameric and octameric complexes were observed. CID of all these species [(αβ)₂, (αβ)₃, and (αβ)₄] predominantly generated highly charged monomers. In addition, we observed hexamer → tetramer + dimer dissociation, implying that hexamers have a tetramer··dimer architecture. Similarly, the observation of octamer → two tetramer dissociation revealed that octamers have a tetramer··tetramer composition. Gas-phase candidate structures of Hb assemblies were produced by molecular dynamics (MD) simulations. Ion mobility spectrometry was used to identify the most likely candidates. Our data reveal that the capability of CID to produce structurally informative subcomplexes depends on the fate of protein-protein interfaces after transfer into the gas phase. Collapse of low affinity interfaces conjoins the corresponding subunits and favors CID via monomer ejection. Structurally informative subcomplexes are formed only if low affinity interfaces do not undergo a major collapse. However, even in these favorable cases CID is still dominated by monomer ejection, requiring careful analysis of the experimental data for the identification of structurally informative subcomplexes.

A GPU-Accelerated Fast Multipole Method for GROMACS: Performance and Accuracy

An important and computationally demanding part of molecular dynamics simulations is the calculation of long-range electrostatic interactions. Today, the prevalent method to compute these interactions is particle mesh Ewald (PME). The PME implementation in the GROMACS molecular dynamics package is extremely fast on individual GPU nodes. However, for large scale multinode parallel simulations, PME becomes the main scaling bottleneck as it requires all-to-all communication between the nodes; as a consequence, the number of exchanged messages scales quadratically with the number of involved nodes in that communication step. To enable efficient and scalable biomolecular simulations on future exascale supercomputers, clearly a method with a better scaling property is required. The fast multipole method (FMM) is such a method. As a first step on the path to exascale, we have implemented a performance-optimized, highly efficient GPU FMM and integrated it into GROMACS as an alternative to PME. For a fair performance comparison between FMM and PME, we first assessed the accuracies of the methods for various sets of input parameters. With parameters yielding similar accuracies for both methods, we determined the performance of GROMACS with FMM and compared it to PME for exemplary benchmark systems. We found that FMM with a multipole order of 8 yields electrostatic forces that are as accurate as PME with standard parameters. Further, for typical mixed-precision simulation settings, FMM does not lead to an increased energy drift with multipole orders of 8 or larger. Whereas an ≈50 000 atom simulation system with our FMM reaches only about a third of the performance with PME, for systems with large dimensions and inhomogeneous particle distribution, e.g., aerosol systems with water droplets floating in a vacuum, FMM substantially outperforms PME already on a single node.

Combining Experimental Data and Computational Methods for the Non-Computer Specialist

Experimental methods are indispensable for the study of the function of biological macromolecules, not just as static structures, but as dynamic systems that change conformation, bind partners, perform reactions, and respond to different stimulus. However, providing a detailed structural interpretation of the results is often a very challenging task. While experimental and computational methods are often considered as two different and separate approaches, the power and utility of combining both is undeniable. The integration of the experimental data with computational techniques can assist and enrich the interpretation, providing new detailed molecular understanding of the systems. Here, we briefly describe the basic principles of how experimental data can be combined with computational methods to obtain insights into the molecular mechanism and expand the interpretation through the generation of detailed models.

Lifetime Considerations for Electrospray Thrusters

Ionic liquid electrospray thrusters are capable of producing microNewton precision thrust at a high thrust–power ratio but have yet to demonstrate lifetimes that are suitable for most missions. Accumulation of propellant on the extractor and accelerator grids is thought to be the most significant life-limiting mechanism. In this study, we developed a life model to examine the effects of design features, operating conditions, and emission properties on the porous accelerator grid saturation time of a thruster operating in droplet emission mode. Characterizing a range of geometries and operating conditions revealed that modifying grid aperture radius and grid spacing by 3–7% can significantly improve thruster lifetime by 200–400%, though a need for explicit mass flux measurement was highlighted. Tolerance analysis showed that misalignment can result in 20–50% lifetime reduction. In addition, examining the impact of electron backstreaming showed that increasing aperture radius produces a significant increase in backstreaming current compared to changing grid spacing. A study of accelerator grid bias voltages revealed that applying a reasonably strong accelerator grid potential (in the order of a kV) can minimize backstreaming current to negligible levels for a range of geometries.

Gas-phase conformations of intrinsically disordered proteins and their complexes with ligands: Kinetically trapped states during transfer from solution to the gas phase

Flexible structures of intrinsically disordered proteins (IDPs) are crucial for versatile functions in living organisms, which involve interaction with diverse partners. Electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) has been widely applied for structural characterization of apo-state and ligand-associated IDPs via two-dimensional separation in the gas phase. Gas-phase IDP structures have been regarded as kinetically trapped states originated from conformational features in solution. However, an implication of the states remains elusive in the structural characterization of IDPs, because it is unclear what structural property of IDPs is preserved. Recent studies have indicated that the conformational features of IDPs in solution are not fully reproduced in the gas phase. Nevertheless, the molecular interactions captured in the gas phase amplify the structural differences between IDP conformers. Therefore, an IDP conformational change that is not observed in solution is observable in the gas-phase structures obtained by ESI-IM-MS. Herein, we have presented up-to-date researches on the key implications of kinetically trapped states in the gas phase with a brief summary of the structural dynamics of IDPs in ESI-IM-MS.

Computational Insights into Compaction of Gas-Phase Protein and Protein Complex Ions in Native Ion Mobility-Mass Spectrometry

Native ion mobility-mass spectrometry (IM-MS) is a rapidly growing field for studying the composition and structure of biomolecules and biomolecular complexes using gas-phase methods. Typically, ions are formed in native IM-MS using gentle nanoelectrospray ionization conditions, which in many cases can preserve condensed-phase stoichiometry. Although much evidence shows that large-scale condensed-phase structure, such as quaternary structure and topology, can also be preserved, it is less clear to what extent smaller-scale structure is preserved in native IM-MS. This review surveys computational and experimental efforts aimed at characterizing compaction and structural rearrangements of protein and protein complex ions upon transfer to the gas phase. A brief summary of gas-phase compaction results from molecular dynamics simulations using multiple common force fields and a wide variety of protein ions is presented and compared to literature IM-MS data.

Role of hydrophobic residues for the gaseous formation of helical motifs

The secondary structure content of proteins and their complexes may change significantly on passing from aqueous solution to the gas phase (as in mass spectrometry experiments). In this work, we investigate the impact of hydrophobic residues on the formation of the secondary structure of a real protein complex in the gas phase. We focus on a well-studied protein complex, the amyloid-β (1-40) dimer (2Aβ). Molecular dynamics simulations reproduce the results of ion mobility-mass spectrometry experiments. In addition, a helix (not present in the solution) is identified involving 19FFAED23, consistent with infrared spectroscopy data on an Aβ segment. Our simulations further point to the role of hydrophobic residues in the formation of helical motifs - hydrophobic sidechains "shield" helices from being approached by residues that carry hydrogen bond sites. In particular, two hydrophobic phenylalanine residues, F19 and F20, play an important role for the helix, which is induced in the gas phase in spite of the presence of two carboxyl-containing residues.

Comparison of ESI-MS/MS and APCI-MS methods for the quantification of folic acid analogs in C. elegans

Folic acid (FA) plays a vital role in central metabolism, including the one carbon cycle, nucleotide, and amino acid biosynthesis. The development of sensitive, accurate analytical methods to measure FA intermediates in tissues is critical to understand their biological roles in diverse physiological and pathological contexts. Here, we developed a highly sensitive method for the simultaneous quantification of FA intermediates in the nematode Caenorhabditis elegans as a model to dissect metabolic networks. The method was further validated by analyzing the worm folate pool upon RNAi knockdown of the dihydrofolate reductase gene dhfr-1. Comparative mass spectrometry behavior of the FA analogs using two different ion sources, electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI), revealed ESI-MS/MS to be more sensitive, but APCI-MS provided more detailed structure inferences, which can elucidate chemical investigation and synthesis of FA analogs. Finally, we report on the use of in vitro oxidation coupled with high-resolution mass spectrometry as a tool to discover new endogenous FA derivatives in the nematode.

Charging and supercharging of proteins for mass spectrometry: recent insights into the mechanisms of electrospray ionization

Molecular dynamics simulations have uncovered mechanistic details of the protein ESI process under various experimental conditions.