Fast Conformational Changes Research Articles

Normal-to-Supercooled Liquid Transition in Molecular Glass-Formers: A Hidden Structural Transformation Fuelled by Conformational Interconversion.

Molecular dynamics and transport coefficients change significantly around the so-called Arrhenius crossover in glass-forming systems. In this article, we revisit the dynamic processes occurring in a glass-forming macrocyclic crown thiaether MeBzS2O above its glass transition, revealing two crossover temperatures: TB at 309 and TA at 333 K. We identify the second one as the Arrhenius crossover that is closely related to the normal-to-supercooled liquid transition in this compound. We show that the transformation occurring at this point goes far beyond molecular dynamics (where the temperature dependence of structural relaxation times changes its character from activation-like to super-Arrhenius), being reflected also in the internal structure and diffraction pattern. In this respect, we found a twofold local organization of the nearest-neighbor molecules via weak van der Waals forces, without the formation of any medium-range order or mesophases. The nearest surrounding of each molecule evolves structurally in time due to the ongoing fast conformational changes. We identify several conformers of MeBzS2O, demonstrating that its lowest-energy conformation is preferred mainly at lower temperatures, i.e., in the supercooled liquid state. Its increased prevalence modifies locally the short-range intermolecular order and promotes vitrification. Consequently, we indicate that the Arrhenius transition is fuelled rather by conformational changes in this glass-forming macrocyclic crown thiaether, which is a different scenario from the so-far existing concepts. Our studies combine broadband dielectric spectroscopy (BDS), X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations.

Log-periodic oscillations as real-time signatures of hierarchical dynamics in proteins.

The time-dependent relaxation of a dynamical system may exhibit a power-law behavior that is superimposed by log-periodic oscillations. D. Sornette [Phys. Rep. 297, 239 (1998)] showed that this behavior can be explained by a discrete scale invariance of the system, which is associated with discrete and equidistant timescales on a logarithmic scale. Examples include such diverse fields as financial crashes, random diffusion, and quantum topological materials. Recent time-resolved experiments and molecular dynamics simulations suggest that discrete scale invariance may also apply to hierarchical dynamics in proteins, where several fast local conformational changes are a prerequisite for a slow global transition to occur. Employing entropy-based timescale analysis and Markov state modeling to a simple one-dimensional hierarchical model and biomolecular simulation data, it is found that hierarchical systems quite generally give rise to logarithmically spaced discrete timescales. By introducing a one-dimensional reaction coordinate that collectively accounts for the hierarchically coupled degrees of freedom, the free energy landscape exhibits a characteristic staircase shape with two metastable end states, which causes the log-periodic time evolution of the system. The period of the log-oscillations reflects the effective roughness of the energy landscape and can, in simple cases, be interpreted in terms of the barriers of the staircase landscape.

Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics.

The potential of molecular simulations is limited by their computational costs. There is often a need to accelerate simulations using some of the enhanced sampling methods. Metadynamics applies a history-dependent bias potential that disfavors previously visited states. To apply metadynamics, it is necessary to select a few properties of the system─collective variables (CVs) that can be used to define the bias potential. Over the past few years, there have been emerging opportunities for machine learning and, in particular, artificial neural networks within this domain. In this broad context, a specific unsupervised machine learning method was utilized, namely, parametric time-lagged t-distributed stochastic neighbor embedding (ptltSNE) to design CVs. The approach was tested on a Trp-cage trajectory (tryptophan cage) from the literature. The trajectory was used to generate a map of conformations, distinguish fast conformational changes from slow ones, and design CVs. Then, metadynamic simulations were performed. To accelerate the formation of the α-helix, we added the α-RMSD collective variable. This simulation led to one folding event in a 350 ns metadynamics simulation. To accelerate degrees of freedom not addressed by CVs, we performed parallel tempering metadynamics. This simulation led to 10 folding events in a 200 ns simulation with 32 replicas.

Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics

Fluorescence correlation spectroscopy is a versatile tool for studying fast conformational changes of biomolecules especially when combined with Förster resonance energy transfer (FRET). Despite the many methods available for identifying structural dynamics in FRET experiments, the determination of the forward and backward transition rate constants and thereby also the equilibrium constant is difficult when two intensity levels are involved. Here, we combine intensity correlation analysis with fluorescence lifetime information by including only a subset of photons in the autocorrelation analysis based on their arrival time with respect to the excitation pulse (microtime). By fitting the correlation amplitude as a function of microtime gate, the transition rate constants from two fluorescence-intensity level systems and the corresponding equilibrium constants are obtained. This shrinking-gate fluorescence correlation spectroscopy (sg-FCS) approach is demonstrated using simulations and with a DNA origami-based model system in experiments on immobilized and freely diffusing molecules. We further show that sg-FCS can distinguish photophysics from dynamic intensity changes even if a dark quencher, in this case graphene, is involved. Finally, we unravel the mechanism of a FRET-based membrane charge sensor indicating the broad potential of the method. With sg-FCS, we present an algorithm that does not require prior knowledge and is therefore easily implemented when an autocorrelation analysis is carried out on time-correlated single-photon data.

Kinetics in DMS: Modeling Clustering and Declustering Reactions.

Differential mobility spectrometry (DMS) uses high-frequency oscillating electrical fields to harness the differential mobility of ions for separating complex sample mixtures prior to detection. To increase the resolving power, a dynamic microsolvation environment is often created by introducing solvent vapors. Here, relatively large clusters are formed at low-field conditions which then evaporate to form smaller clusters at high-field conditions. The kinetics of these processes as the electrical field strength oscillates are not well studied. Here, we develop a computational framework to investigate how the different reactions (cluster association, cluster dissociation, and fast conformational changes) behave at different field strengths. We aim to better understand these processes, their effect on experimental outcomes, and whether DMS model accuracy is improved via incorporating their description. We find that cluster association and dissociation reactions for typical ion-solvent pairs are fast compared to the time scale of the varying separation fields usually used. However, low solvent concentration, small dipole moments, and strong ion-solvent binding can result in reaction rates small enough that a lag is observed in the ion's DMS response. This can yield differences of several volts in the compensation voltages required to correct ion trajectories for optimal transmission. We also find that the proposed kinetic approach yields generally better agreement with experiment than using a modified Boltzmann weighting scheme. Thus, this work provides insights into the chemical dynamics occurring within the DMS cell while also increasing the accuracy of dispersion plot predictions.

Aggregation of Lactoferrin Caused by Droplet Atomization Process via a Two-Fluid Nozzle: The Detrimental Effect of Air-Water Interfaces.

Biological macromolecules, especially therapeutic proteins, are delicate and highly sensitive to denaturation from stresses encountered during the manufacture of dosage forms. Thin-film freeze-drying (TFFD) and spray freeze-drying (SFD) are two processes used to convert liquid forms of protein into dry powders. In the production of inhalable dry powders that contain proteins, these potential stressors fall into three categories based on their occurrence during the primary steps of the process: (1) droplet formation (e.g., the mechanism of droplet formation, including spray atomization), (2) freezing, and (3) frozen water removal (e.g., sublimation). This study compares the droplet formation mechanism used in TFFD and SFD by investigating the effects of spraying on the stability of proteins, using lactoferrin as a model. This study considers various perspectives on the denaturation (e.g., conformation) of lactoferrin after subjecting the protein solution to the atomization process using a pneumatic two-fluid nozzle (employed in SFD) or a low-shear drop application through the nozzle. The surface activity of lactoferrin was examined to explore the interfacial adsorption tendency, diffusion, and denaturation process. Subsequently, this study also investigates the secondary and tertiary structure of lactoferrin and the quantification of monomers, oligomers, and, ultimately, aggregates. The spraying process affected the tertiary structure more negatively than the tightly woven secondary structure, resulting in the peak position corresponding to the tryptophan (Trp) residues red-shifting by 1.5 nm. This conformational change can either (a) be reversed at low concentrations via relaxation or (b) proceed to form irreversible aggregates at higher concentrations. Interestingly, when the sample was allowed to progress into micrometer-sized aggregates, such a dramatic change was not detected using methods such as size-exclusion chromatography, polyacrylamide gel electrophoresis, and dynamic light scattering at 173°. A more complete understanding of the heterogeneous protein sample was achieved only through a combination of 173 and 13° backward and forward scattering, a combination of derived count rate measurements, and microflow imaging (MFI). After studying the impact of droplet formation mechanisms on aggregation tendency of lactoferrin, we further investigated two additional model proteins with different surface activity: bovine IgG (serving as a non surface-active negative reference), and β-galactosidase (another surface-active protein). The results corroborated the lactoferrin findings that spray-atomization-related stress-induced protein aggregation was much more pronounced for proteins that are surface active (lactoferrin and β-galactosidase), but it was minimal for non-surface-active protein (bovine IgG). Finally, compared to the low-shear dripping used in the TFFD process, lactoferrin underwent a relatively fast conformational change upon exposure to the high air-water interface of the two-fluid atomization nozzle used in the SFD process as compared to the low shear dripping used in the TFFD process. The interfacial-induced denaturation that occurred during spraying was governed primarily by the size of the atomized droplets, regardless of the duration of exposure to air. The percentage of denatured protein population and associated activity loss, in the case of β-galactosidase, was determined to range from 2 to 10% depending on the air-flow rate of the spraying process.

Ambipolar diarylnitroxides: Molecular design and electrochemical testing

AbstractPossible approaches to molecular design of stable diarylnitroxyl radicals capable to form sufficiently stable cations and anions under one‐electron oxidation and reduction are discussed. Both covalent and noncovalent stabilizing “tools” are considered. The main focus is made on the dynamic stabilization of oppositely charged redox states of a molecule through conformational changes. The efficiency of the approaches was confirmed on a wide range of novel diarylnitroxides designed accordingly to the suggested guidelines. Spectral and quantum‐chemical data support fast conformational changes accompanying electron transfer steps and facilitating stabilization of the cationic and anionic species. Voltammetric study of new compounds revealed the formation of reversible redox couples in both anodic and cathodic areas for the majority of nitroxides making them suitable for practical application.

Building and Using a Two-Photon Fluorescence Cross-Correlation Spectroscopy Setup Including Fluorescence Lifetime Analysis.

Fluorescence Cross-Correlation Spectroscopy (FCCS) is a well-established and useful tool in physics and chemistry. Furthermore, due to its hybrid character of being a bulk assay at a single molecular level, it found many applications in biophysics and molecular biochemistry. Examples may be investigating kinetics and dynamics of chemical and biochemical reactions suchas protein-ligand-, protein-protein-binding, fast conformational changes, and intracellular transportation. Also, it was utilized to characterize larger structures suchas lipid vesicles and multi-protein complexes. A two-photon excitation source makes FCCS relatively easy-to-use and easy-to-maintain. Combining this technique with fluorescence lifetime analysis results in a versatile biophysical tool that can be used to solve many biological problems, as even small changes in the local environment, like pH or salt concentration, can be monitored if appropriate fluorophores are used. An example of its use for membrane docking and fusion assays is described in Chap. 13 . In this chapter, we want to give the reader a simple, detailed step-by-step guideof how to set up such a tool.

Kinetic analysis of ASIC1a delineates conformational signaling from proton-sensing domains to the channel gate

Acid-sensing ion channels (ASICs) are neuronal Na+ channels that are activated by a drop in pH. Their established physiological and pathological roles, involving fear behaviors, learning, pain sensation, and neurodegeneration after stroke, make them promising targets for future drugs. Currently, the ASIC activation mechanism is not understood. Here, we used voltage-clamp fluorometry (VCF) combined with fluorophore-quencher pairing to determine the kinetics and direction of movements. We show that conformational changes with the speed of channel activation occur close to the gate and in more distant extracellular sites, where they may be driven by local protonation events. Further, we provide evidence for fast conformational changes in a pathway linking protonation sites to the channel pore, in which an extracellular interdomain loop interacts via aromatic residue interactions with the upper end of a transmembrane helix and would thereby open the gate.

The Transport Cycle of a Sodium/Proton Antiporter

Sodium/proton antiporters, also known as sodium/proton exchangers, are essential secondary active transporters that are involved in pH homeostasis and regulation of sodium concentration and cell volume. They belong to the monovalent cation/proton antiporter families (CPA1 and CPA2) which all appear to share a common fold, spanning prokaryotic to mammalian family members. They obey general principles of secondary active transporters, namely they switch between at least two conformations in accordance with the alternating access model, the major states (outward facing (OF) and inward facing (OF)) are rooted in structurally breaking an inverted repeat symmetry, and they transduce energy from a driving ion gradient to vectorial substrate transport through conformational cycles. However, these broad principles constrain but do not immediately provide insights into the molecular mechanism of sodium/proton antiport. We have been using molecular dynamics simulations (long equilibrium MD, free energy calculations, enhanced sampling for rare events, constant pH simulations) in combination with experimental techniques such as X-ray crystallography and functional measurements to investigate key steps in the transport cycle of the prokaryotic CPA2 transporter TtNapA. A competitive binding mechanism between protons and sodium emerges from an analysis of the thermodynamics of the OF and IF states and naturally explains the experimentally observed activity peak in a narrow pH range. Direct computational sampling of the conformational transitions shows that NapA can undergo fast (sub-microsecond) conformational changes in either the proton or sodium-loaded states and reveals a distinct meta-stable intermediate state. Taken together, the information from all the major steps in the complete transport cycle can then form the basis for multi-scale kinetic models of the physiological function of the antiporter.

Molecular Insight into Cu2+-Induced Conformational Transitions of Amyloid β-Protein from Fast Kinetic Analysis and Molecular Dynamics Simulations.

Cu2+-mediated amyloid β-protein (Aβ) aggregation is implicated in the pathogenesis of Alzheimer's disease, so it is of significance to understand Cu2+-mediated conformational transitions of Aβ. Herein, four Aβ mutants were created by using the environment-sensitive cyanophenylalanine to respectively substitute F4, Y10, F19, and F20 residues of Aβ40. By using stopped-flow fluorescence spectroscopy and molecular dynamics (MD) simulations, the early stage conformational transitions of the mutants mediated by Cu2+ binding were investigated. The fast kinetics unveils that Cu2+ has more significant influence on the conformational changes of N-terminal (F4 and Y10) than on the central hydrophobic core (CHC, F19, and F20) under different pH conditions (pH 6.6-8.0), especially Y10. Interestingly, lag periods of the conformational transitions are observed for the F19 and F20 mutants at pH 8.0, indicating the slow response of the two mutation sites on the conformational transitions. More importantly, significantly longer lag periods for F20 than for F19 indicate the conduction of the transition from F19 to F20. The conduction time (difference in lag period) decreases from 4.5 s at Cu2+ = 0 to undetectable (<1 ms) at Cu2+ = 10 μM. The significant difference in the response time of F19 and F20 and the fast local conformational changes of Y10 imply that the conformational transitions of Aβ start around Y10. MD simulations support the observation of hydrophobicity increase at N-terminal during the conformational transitions of Aβ-Cu2+. It also reveals that Y10 is immediately approached by Cu2+, supporting the speculation that the starting point of conformational transitions of Aβ is near Y10. The work has provided molecular insight into the early stage conformational transitions of Aβ40 mediated by Cu2+.

Rationalization of chirality transfer and fast conformational changes in a tris(2-pyridylmethyl)amine-based cage.

The key features that govern the chirality transfer in a structurally contracted covalent cage, consisting of a northern chiral cyclotriveratrylene (CTV) connected to a southern tris(2-pyridyl-methyl)amine (TPA) unit by three methyl bridges, are described. The preferential orientation of the propeller arrangement of TPA is dictated by its compact structure, with an arm of the TPA unit pointing inside the cage, together with the relative positioning of the three pyridines regarding the chiral CTV cap. The diastereomers with P/P (or M/M) configurations for the CTV and TPA units adopt eclipsed structures and were found to be more stable by 40 kJ mol−1 than the P/M (or M/P) diastereomer which displays a staggered arrangement. The existence of isomerization pathways between isomers of the cage with low energy barriers (38 kJ mol−1) accounts for the 1H-NMR signal, which is consistent with an averaged C3 structure.

Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations.

Experiments face challenges in the analysis of intrinsically disordered proteins in solution due to fast conformational changes and enhanced aggregation propensity. Computational studies complement experiments, being widely used in the analyses of intrinsically disordered proteins, especially those positioned at the centers of neurodegenerative diseases. However, recent investigations - including our own - revealed that computer simulations face significant challenges and limitations themselves. In this review, we introduced and discussed some of the scientific challenges and limitations of computational studies conducted on intrinsically disordered proteins. We also outlined the importance of future developments in the areas of computational chemistry and computational physics that would be needed for generating more accurate data for intrinsically disordered proteins from computer simulations. Additional theoretical strategies that can be developed are discussed herein.

Broad-Band Ultraviolet CD Spectroscopy of Ultrafast Peptide Backbone Conformational Dynamics.

The far-UV spectral window widely used for the conformational analysis of biomolecules is not easily covered with broad-band lasers. This has made it difficult to use circular dichroism (CD) spectroscopy to directly follow fast structure changes. By combining transient CD spectroscopy in the deep-UV with thioamide substitution, we demonstrate a method to overcome this difficulty. We investigated a dipeptide whose two carbonyl oxygen atoms were replaced by sulfur, red-shifting the strong lowest-lying ππ* transitions into the more accessible 250-370 nm spectral window. Coupling of the two thioamide units cannot be resolved by achiral 2D-UV spectroscopy, but it gives rise to a pronounced bisignate CD spectrum. The transient CD spectra reveal weakening of this coupling in the electronically excited state, where conformational constraints are released. Our results show that direct local probing of fast backbone conformational change via CD spectroscopy is possible in combination with site-selective thio substitution in peptides and proteins.

Synthesis, Structures and DFT Computational Studies of [3.1.1]Metacyclophanes Containing Benzofuran Rings

Abstract[3.1.1]Metacyclophane ([3.1.1]MCP) 6 a containing two benzofuran rings was obtained by treatment of [3.3.3]MCP‐dione 5 with trimethylsilyl iodide. The precursor 5 was synthesized using (p‐tolylsulfonyl)methyl isocyanide (TosMIC) as the cyclization reagent. The 1H‐NMR spectrum of 6 a at room temperature reveals that it undergoes very fast conformational changes relative to the NMR time scale and that the phenolic hydrogen forms weak intramolecular hydrogen bonding with the oxygen of one of the benzofurans. O‐Methylation of 6 a afforded the calixarene analogue, macrocyclic [3.1.1]MCP 7 a whose 1H‐NMR spectrum reveals that it adopts a cone‐likeconformation in solution at room temperature and the alkoxy group is pointing above and away from the macrocyclic cavity.

Revisiting Cu(II) Bound Amyloid-β40 and Amyloid-β42 Peptides: Varying Coordination Chemistries

Metal ions and intrinsically disordered peptides amyloid-β40 and amyloid-β42 are at the center of Alzheimer´s disease pathology. Divalent copper ion binds to amyloid-β40 and amyloid-β42 peptides with varying coordination chemistries. Experiments face challenges in the measurements of divalent copper ion bound monomeric amyloid-β40 and amyloid-β42 in an aqueous solution medium because of fast conformational changes, rapid aggregation processes and solvent effects. Theoretical studies complement experiments and provide insights at the atomic and molecular levels with dynamics. However, until recently, potential functions for simulating divalent copper ion bound amyloid-β40 and amyloid-β42 peptides with varying coordination chemistries were lacking. Using new potential functions that were developed for divalent copper centers, Cu(II), including three histidine residues and an oxygen-ligated amino acid residue, the structures and thermodynamic properties of Cu(II)-bound amyloid-β40 and amyloid-β42 peptides in an aqueous solution medium were studied. For these purposes, extensive first principles calculations and replica exchange molecular dynamics simulations were conducted. In this study, the secondary and tertiary structural properties, conformational Gibbs free energy values, potential of mean force surfaces, salt bridges and aggregation propensities of aqueous Cu(II)-bound amyloid-β40 and amyloid-β42 peptides are presented. Different than previous findings in the literature, results clearly show that the coordination chemistry variations impact the structural and thermodynamic properties of divalent Cu(II) bound amyloid-β alloforms in water. Specificities about these differences are revealed in this study at the atomic level with dynamics. Results presented herein are the first to offer a comparison of the monomeric Cu(II)-bound amyloid-β40 and amyloid-β42 peptides with varying coordination chemistries using bonded model potential functions.

Conformational Dynamics of DNA Repair by Escherichia coli Endonuclease III

Escherichia coli endonuclease III (Endo III or Nth) is a DNA glycosylase with a broad substrate specificity for oxidized or reduced pyrimidine bases. Endo III possesses two types of activities: N-glycosylase (hydrolysis of the N-glycosidic bond) and AP lyase (elimination of the 3'-phosphate of the AP-site). We report a pre-steady-state kinetic analysis of structural rearrangements of the DNA substrates and uncleavable ligands during their interaction with Endo III. Oligonucleotide duplexes containing 5,6-dihydrouracil, a natural abasic site, its tetrahydrofuran analog, and undamaged duplexes carried fluorescent DNA base analogs 2-aminopurine and 1,3-diaza-2-oxophenoxazine as environment-sensitive reporter groups. The results suggest that Endo III induces several fast sequential conformational changes in DNA during binding, lesion recognition, and adjustment to a catalytically competent conformation. A comparison of two fluorophores allowed us to distinguish between the events occurring in the damaged and undamaged DNA strand. Combining our data with the available structures of Endo III, we conclude that this glycosylase uses a multistep mechanism of damage recognition, which likely involves Gln(41) and Leu(81) as DNA lesion sensors.

High-speed angle-resolved imaging of a single gold nanorod with microsecond temporal resolution and one-degree angle precision.

We developed two types of high-speed angle-resolved imaging methods for single gold nanorods (SAuNRs) using objective-type vertical illumination dark-field microscopy and a high-speed CMOS camera to achieve microsecond temporal and one-degree angle resolution. These methods are based on: (i) an intensity analysis of focused images of SAuNR split into two orthogonally polarized components and (ii) the analysis of defocused SAuNR images. We determined the angle precision (statistical error) and accuracy (systematic error) of the resultant SAuNR (80 nm × 40 nm) images projected onto a substrate surface (azimuthal angle) in both methods. Although both methods showed a similar precision of ∼1° for the azimuthal angle at a 10 μs temporal resolution, the defocused image analysis showed a superior angle accuracy of ∼5°. In addition, the polar angle was also determined from the defocused SAuNR images with a precision of ∼1°, by fitting with simulated images. By taking advantage of the defocused image method's full revolution measurement range in the azimuthal angle, the rotation of the rotary molecular motor, F1-ATPase, was measured with 3.3 μs temporal resolution. The time constants of the pauses waiting for the elementary steps of the ATP hydrolysis reaction and the torque generated in the mechanical steps have been successfully estimated. The high-speed angle-resolved SAuNR imaging methods will be applicable to the monitoring of the fast conformational changes of many biological molecular machines.

Probing Protein Interactions of Cyanylated Acyl Carrier Proteins using Vibrational Spectroscopy

Acyl carrier proteins (ACPs) are highly conserved protein domains involved in the synthesis of polyketides, natural products essential to pharmaceutical drug development. ACPs are part of a multicomponent modular system known as polyketide synthases (PKSs). Understanding these systems permits the manipulation of PKSs to produce “unnatural” natural compounds essential for combating health issues. ACPs interact with PKS domains through a flexible 4′phosphopantetheine (4′-Ppant) prosthetic arm that undergoes important and fast conformational changes difficult to track with NMR and X-ray crystallography. We installed a thiocyanate (-SCN) probe on the terminal thiol of a 4′ Ppant arm to observe these conformations on a picosecond time scale. The method enables the identification of factors affecting 4′ Ppant arm movement. We observed the effects on 6-deoxyerythronolide B synthase (DEBS) and fatty acid synthase (FAS) ACP conformation when titrated with their respective catalytic ketosynthase (KS) partners. Vibrational spectroscopy reveals that dynamic protein-protein interactions as well as substrate chain length perturb the conformation and location of the 4′ Ppant arm.

Protein flexibility and cysteine reactivity: influence of mobility on the H-bond network and effects on pKa prediction.

Thanks to its chemical plasticity, cysteine (Cys) is a very versatile player in proteins. A major determinant of Cys reactivity is pKa: the ability to predict it is deemed critical in redox bioinformatics. I considered different computational methods for pKa predictions and ultimately applied one (propka, ppka1) to various datasets; for all residues I assessed the effect of (1) hydrogen bonding, electrostatics and solvation on predictions and (2) protein mobility on pKa variability. Particularly for Cys, exposure and H-bond contributions heavily dictated propka predictions. The prominence of H-bond contributions was previously reported: this may explain the effectiveness of ppka1 (with Cys, tested in a benchmark). However ppka1 was also very sensitive to protein mobility; I assessed the effects of mobility on particularly large (compared to previous studies) datasets of structural ensembles; I found that exposed Cys presented the highest pKa variability, ascribable to correspondingly high H-bond fluctuations associated with protein flexibility. The benefit of including protein dynamics in pKa predictions was previously proposed, but empirical methods were never tested in this sense; instead, giving their outstanding speed, they could lend particularly well to this purpose. I devised a strategy combining short range molecular dynamics with ppka1; the protocol aimed to mitigate high ppka1 variability by including a "statistical view" of fast conformational changes. Tested in a benchmark, the strategy lead to improved performances. These results provide new insights on Cys bioinformatics (pKa prediction protocols) and Cys biology (effect of mobility on exposed Cys properties).