System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields.

The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer (CT) and polarization (POL) effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding CT and POL. Furthermore, we present an open-source parametrization tool, called FFAFFURR, that enables the (system-specific) parametrization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a zinc-finger protein.

Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic.

We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.

Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic.

We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.

Impact of anion polarizability on ion pairing in microhydrated salt clusters.

Despite longstanding interest in the mechanism of salt dissolution in aqueous media, a molecular level understanding remains incomplete. Here, cryogenic ion trap vibrational action spectroscopy is combined with electronic structure calculations to track salt hydration in a gas phase model system one water molecule at a time. The infrared photodissociation spectra of microhydrated lithium dihalide anions [LiXX'(H2O) n ]- (XX' = I2, ClI and Cl2; n = 1-3) in the OH stretching region (3800-2800 cm-1) provide a detailed picture of how anion polarizability influences the competition among ion-ion, ion-water and water-water interactions. While exclusively contact ion pairs are observed for n = 1, the formation of solvent-shared ion pairs, identified by markedly red-shifted OH stretching bands (<3200 cm-1), originating from the bridging water molecules, is favored already for n = 2. For n = 3, Li+ reaches its maximum coordination number of four only in [LiI2(H2O)3]-, in accordance with the hard and soft Lewis acid and base principle. Water-water hydrogen bond formation leads to a different solvent-shared ion pair motif in [LiI2(H2O)3]- and network formation even restabilizes the contact ion pair motif in [LiCl2(H2O)3]-. Structural assignments are exclusively possible after the consideration of anharmonic effects. Molecular dynamics simulations confirm that the significance of large amplitude motion (of the water molecules) increases with increasing anion polarizability and that needs to be considered already at cryogenic temperatures.

Better force fields start with better data: A data set of cation dipeptide interactions.

We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids - including alternative possible side chain protonation states and their interactions with selected divalent cations (Ca2+, Mg2+ and Ba2+). The data covers 21,909 stationary points on the respective potential-energy surfaces in a wide relative energy range of up to 4 eV (390 kJ/mol). Relevant properties of interest, like partial charges, were derived for the conformers. The motivation was to provide a solid data basis for force field parameterization and further applications like machine learning or benchmarking. In particular the process of creating all this data on the same first-principles footing, i.e. density-functional theory calculations employing the generalized gradient approximation with a van der Waals correction, makes this data suitable for first principles data-driven force field development. To make the data accessible across domain borders and to machines, we formalized the metadata in an ontology.

Benchmarking polarizable and non-polarizable force fields for Ca2+-peptides against a comprehensive QM dataset.

Explicit description of atomic polarizability is critical for the accurate treatment of inter-molecular interactions by force fields (FFs) in molecular dynamics (MD) simulations aiming to investigate complex electrostatic environments such as metal-binding sites of metalloproteins. Several models exist to describe key monovalent and divalent cations interacting with proteins. Many of these models have been developed from ion-amino-acid interactions and/or aqueous-phase data on cation solvation. The transferability of these models to cation-protein interactions remains uncertain. Herein, we assess the accuracy of existing FFs by their abilities to reproduce hierarchies of thousands of Ca2+-dipeptide interaction energies based on density-functional theory calculations. We find that the Drude polarizable FF, prior to any parameterization, better approximates the QM interaction energies than any of the non-polarizable FFs. Nevertheless, it required improvement in order to address polarization catastrophes where, at short Ca2+-carboxylate distances, the Drude particle of oxygen overlaps with the divalent cation. To ameliorate this, we identified those conformational properties that produced the poorest prediction of interaction energies to reduce the parameter space for optimization. We then optimized the selected cation-peptide parameters using Boltzmann-weighted fitting and evaluated the resulting parameters in MD simulations of the N-lobe of calmodulin. We also parameterized and evaluated the CTPOL FF, which incorporates charge-transfer and polarization effects in additive FFs. This work shows how QM-driven parameter development, followed by testing in condensed-phase simulations, may yield FFs that can accurately capture the structure and dynamics of ion-protein interactions.

Structure and Reactivity of Al-O(H)-Al Moieties in Siloxide Frameworks: Solution and Gas-Phase Model Studies.

Even though aluminas and aluminosilicates have found widespread application, a consistent molecular understanding of their surface heterogeneity and the behavior of defects resulting from hydroxylation/dehydroxylation remains unclear. Here, we study the well-defined molecular model compound, [Al3 (µ2 -OH)3 (THF)3 (PhSi(OSiPh2 O)3 )2 ], 1, to gain insight into the acid-base reactivity of cyclic trinuclear Al3 (µ2 -OH)3 moieties at the atomic level. We find that, like zeolites, they are sufficiently acidic to catalyze the isomerization of olefins. DFT and gas phase vibrational spectroscopy on solvent-free and deprotonated 1 show that the six-membered ring structure of its Al3 (µ2 -OH)3 core is unstable with respect to deprotonation of one of its hydroxy groups and rearranges into two edge-sharing four-membered rings. This renders AlIV -O(H)-AlIV units strong acid sites, and all results together suggest that their acidity is similar to that of zeolitic SiIV -O(H)-AlIV groups.

Probing chirality recognition of protonated glutamic acid dimers by gas-phase vibrational spectroscopy and first-principles simulations.

The homochirality of the amino acid metabolism still puzzles biochemists. Vibrational spectroscopy of mass-selected gas-phase amino acids and their clusters can precisely reveal their conformation and might ultimately help to decode the interactions responsible for chirality recognition. Infrared photodissociation (IRPD) and conformer-selective IR-IR hole burning spectra of protonated glutamic acid dimers (LL-/LD-Glu2H+) recorded in the fingerprint and XH stretch ranges (1100-1900 and 2600-3600 cm-1) provide direct insight into their stereospecific interactions. Glu2H+ dimers are generated by electrospray ionization and stored in a cryogenic quadrupole ion trap held at 10 K. The assignment of the IRPD spectra is supported by vibrational analysis using many-body dispersion-corrected hybrid density-functional theory. Sampling of the conformational space is accomplished by basin hopping and replica-exchange molecular dynamics simulations. The most stable LD-Glu2H+ dimer (LD1) is predicted to be more stable than the most stable LL-Glu2H+ dimer (LL1) by ΔE0 = 4.0 kJ mol-1, which relies on stronger secondary interactions in LD1 as demonstrated by the noncovalent interaction method. IR-IR hole burning spectroscopy reveals the coexistence of at least four LD-Glu2H+ and three LL-Glu2H+ conformers. Their IR-dip spectra are assigned to the most stable conformers at room and cryogenic temperature, revealing incomplete thermalization of the ions by kinetic trapping in the cold trap. We observe different population ratios of LL and LD conformers of Glu2H+, as revealed by specific νNH2 and νCO intensities (fingerprints of chirality recognition).

The Structure of the Protonated Serine Octamer.

The amino acid serine has long been known to form a protonated "magic-number" cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretical studies, there is no consensus on a Ser8H+ structure that is in agreement with all experimental observations. Here, we present the structure of Ser8H+ determined by a combination of infrared spectroscopy and ab initio molecular dynamics simulations. The three-dimensional structure that we determine is ∼25 kcal mol-1 more stable than the previous most stable published structure and explains both the homochiral preference and the experimentally observed facile replacement of two serine units.

Autoregulation of von Willebrand factor function by a disulfide bond switch.

Force-dependent binding of platelet glycoprotein Ib (GPIb) receptors to plasma von Willebrand factor (VWF) plays a key role in hemostasis and thrombosis. Previous studies have suggested that VWF activation requires force-induced exposure of the GPIb binding site in the A1 domain that is autoinhibited by the neighboring A2 domain. However, the biochemical basis of this "mechanopresentation" remains elusive. From a combination of protein chemical, biophysical, and functional studies, we find that the autoinhibition is controlled by the redox state of an unusual disulfide bond near the carboxyl terminus of the A2 domain that links adjacent cysteine residues to form an eight-membered ring. Only when the bond is cleaved does the A2 domain bind to the A1 domain and block platelet GPIb binding. Molecular dynamics simulations indicate that cleavage of the disulfide bond modifies the structure and molecular stresses of the A2 domain in a long-range allosteric manner, which provides a structural explanation for redox control of the autoinhibition. Significantly, the A2 disulfide bond is cleaved in ~75% of VWF subunits in healthy human donor plasma but in just ~25% of plasma VWF subunits from heart failure patients who have received extracorporeal membrane oxygenation support. This suggests that the majority of plasma VWF binding sites for platelet GPIb are autoinhibited in healthy donors but are mostly available in heart failure patients. These findings demonstrate that a disulfide bond switch regulates mechanopresentation of VWF.

About Underappreciated Yet Active Conformations of Thiourea Organocatalysts.

Conformational dynamics can define the function of organocatalysts. While the accepted mechanism of Schreiner's catalyst features a double hydrogen bond to the substrate that only forms with the anti-anti conformation of its central thiourea group, our electronic-structure theory study reveals that binding of the model substrate methyl vinyl ketone prefers syn-anti conformations. We find a new mechanism featuring π stacking interactions and highlight the need for extensive structure searches for flexible molecules, especially when aiming for structure-based design of catalytic activity.

Kinetically Trapped Liquid-State Conformers of a Sodiated Model Peptide Observed in the Gas Phase.

We investigate the peptide AcPheAla5LysH+, a model system for studying helix formation in the gas phase, in order to fully understand the forces that stabilize the helical structure. In particular, we address the question of whether the local fixation of the positive charge at the peptide's C-terminus is a prerequisite for forming helices by replacing the protonated C-terminal Lys residue by Ala and a sodium cation. The combination of gas-phase vibrational spectroscopy of cryogenically cooled ions with molecular simulations based on density-functional theory (DFT) allows for detailed structure elucidation. For sodiated AcPheAla6, we find globular rather than helical structures, as the mobile positive charge strongly interacts with the peptide backbone and disrupts secondary structure formation. Interestingly, the global minimum structure from simulation is not present in the experiment. We interpret that this is due to high barriers involved in rearranging the peptide-cation interaction that ultimately result in kinetically trapped structures being observed in the experiment.

Mapping and classifying molecules from a high-throughput structural database.

High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from computational searches, as well as the agglomeration of data of heterogeneous provenance leads to considerable challenges when it comes to navigating the database, representing its structure at a glance, understanding structure-property relations, eliminating duplicates and identifying inconsistencies. Here we present a case study, based on a data set of conformers of amino acids and dipeptides, of how machine-learning techniques can help addressing these issues. We will exploit a recently-developed strategy to define a metric between structures, and use it as the basis of both clustering and dimensionality reduction techniques-showing how these can help reveal structure-property relations, identify outliers and inconsistent structures, and rationalise how perturbations (e.g. binding of ions to the molecule) affect the stability of different conformers.

Mutation G1629E Increases von Willebrand Factor Cleavage via a Cooperative Destabilization Mechanism.

The large multimeric glycoprotein von Willebrand Factor (VWF) plays a pivotal adhesive role during primary hemostasis. VWF is cleaved by the protease ADAMTS13 as a down-regulatory mechanism to prevent excessive VWF-mediated platelet aggregation. For each VWF monomer, the ADAMTS13 cleavage site is located deeply buried inside the VWF A2 domain. External forces in vivo or denaturants in vitro trigger the unfolding of this domain, thereby leaving the cleavage site solvent-exposed and ready for cleavage. Mutations in the VWF A2 domain, facilitating the cleavage process, cause a distinct form of von Willebrand disease (VWD), VWD type 2A. In particular, the VWD type 2A Gly1629Glu mutation drastically accelerates the proteolytic cleavage activity, even in the absence of forces or denaturants. However, the effect of this mutation has not yet been quantified, in terms of kinetics or thermodynamics, nor has the underlying molecular mechanism been revealed. In this study, we addressed these questions by using fluorescence correlation spectroscopy, molecular dynamics simulations, and free energy calculations. The measured enzyme kinetics revealed a 20-fold increase in the cleavage rate for the Gly1629Glu mutant compared with the wild-type VWF. Cleavage was found cooperative with a cooperativity coefficient n = 2.3, suggesting that the mutant VWF gives access to multiple cleavage sites of the VWF multimer at the same time. According to our simulations and free energy calculations, the Gly1629Glu mutation causes structural perturbation in the A2 domain and thereby destabilizes the domain by ∼10 kJ/mol, promoting its unfolding. Taken together, the enhanced proteolytic activity of Gly1629Glu can be readily explained by an increased availability of the ADAMTS13 cleavage site through A2-domain-fold thermodynamic destabilization. Our study puts forward the Gly1629Glu mutant as a very efficient enzyme substrate for ADAMTS13 activity assays.

Mutual A domain interactions in the force sensing protein von Willebrand factor.

The von Willebrand factor (VWF) is a glycoprotein in the blood that plays a central role in hemostasis. Among other functions, VWF is responsible for platelet adhesion at sites of injury via its A1 domain. Its adjacent VWF domain A2 exposes a cleavage site under shear to degrade long VWF fibers in order to prevent thrombosis. Recently, it has been shown that VWF A1/A2 interactions inhibit the binding of platelets to VWF domain A1 in a force-dependent manner prior to A2 cleavage. However, whether and how this interaction also takes place in longer VWF fragments as well as the strength of this interaction in the light of typical elongation forces imposed by the shear flow of blood remained elusive. Here, we addressed these questions by using single molecule force spectroscopy (SMFS), Brownian dynamics (BD), and molecular dynamics (MD) simulations. Our SMFS measurements demonstrate that the A2 domain has the ability to bind not only to single A1 domains but also to VWF A1A2 fragments. SMFS experiments of a mutant [A2] domain, containing a disulfide bond which stabilizes the domain against unfolding, enhanced A1 binding. This observation suggests that the mutant adopts a more stable conformation for binding to A1. We found intermolecular A1/A2 interactions to be preferred over intramolecular A1/A2 interactions. Our data are also consistent with the existence of two cooperatively acting binding sites for A2 in the A1 domain. Our SMFS measurements revealed a slip-bond behavior for the A1/A2 interaction and their lifetimes were estimated for forces acting on VWF multimers at physiological shear rates using BD simulations. Complementary fitting of AFM rupture forces in the MD simulation range adequately reproduced the force response of the A1/A2 complex spanning a wide range of loading rates. In conclusion, we here characterized the auto-inhibitory mechanism of the intramolecular A1/A2 bond as a shear dependent safeguard of VWF, which prevents the interaction of VWF with platelets.

Assessing the Accuracy of Across-the-Scale Methods for Predicting Carbohydrate Conformational Energies for the Examples of Glucose and α-Maltose.

A big hurdle when entering the field of carbohydrate research stems from the complications in the analytical and computational treatment. In effect, this extremely important class of biomolecules remains underinvestigated when compared, for example, with the maturity of genomics and proteomics research. On the theory side, the commonly used empirical methods suffer from an insufficient amount of high-quality experimental data against which they can be thoroughly validated. In order to provide a pivotal point for an ascent of accurate carbohydrate simulations, we present here a structure/energy benchmark set of diverse glucose (in three isomeric forms) and α-maltose conformations at the coupled-cluster level as well as an assessment of commonly used energy functions. We observe that empirical force fields and semiempirical approaches, on average, do not reproduce accurately the reference energy hierarchies. While the force fields maintain accuracy for the low-energy structures, the semiempirical methods perform unsatisfactory for the entire range. On the contrary, density-functional approximations reproduce the reference energy hierarchies with better than chemical accuracy already at the generalized gradient approximation level (GGA). Particularly, the novel meta-GGA functional SCAN provides the accuracy of more expensive hybrid functionals at fraction of their computational cost. In conclusion, we advocate for electronic-structure theory methods to become the routine tool for simulations of carbohydrates.

Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor.

We here give information for a deeper understanding of single molecule force spectroscopy (SMFS) data through the example of the blood protein von Willebrand factor (VWF). It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD) loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently developed model by Bullerjahn, Sturm, and Kroy (BSK) was used for this demonstration. Further, Brownian dynamics (BD) simulations, which can be utilized to estimate the lifetimes of intramolecular VWF interactions under physiological shear, are described. For interpretation and discussion of the methods and data presented here, we would like to directly point the reader to the related research paper, "Mutual A domain interactions in the force sensing protein von Willebrand Factor" (Posch et al., 2016) [1].

Conformations of Prolyl-Peptide Bonds in the Bradykinin 1-5 Fragment in Solution and in the Gas Phase.

The dynamic nature of intrinsically disordered peptides makes them a challenge to characterize by solution-phase techniques. In order to gain insight into the relation between the disordered state and the environment, we explore the conformational space of the N-terminal 1-5 fragment of bradykinin (BK[1-5](2+)) in the gas phase by combining drift tube ion mobility, cold-ion spectroscopy, and first-principles simulations. The ion-mobility distribution of BK[1-5](2+) consists of two well-separated peaks. We demonstrate that the conformations within the peak with larger cross-section are kinetically trapped, while the more compact peak contains low-energy structures. This is a result of cis-trans isomerization of the two prolyl-peptide bonds in BK[1-5](2+). Density-functional theory calculations reveal that the compact structures have two very different geometries with cis-trans and trans-cis backbone conformations. Using the experimental CCSs to guide the conformational search, we find that the kinetically trapped species have a trans-trans configuration. This is consistent with NMR measurements performed in a solution, which show that 82% of the molecules adopt a trans-trans configuration and behave as a random coil.