Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion

Dynamic Personality of Proteins and Effect of the Molecular Environment

Protein dynamics display distinct traits that are linked to their specific biological function. However, the interplay between intrinsic dynamics and the molecular environment on protein stability remains poorly understood. In this study, we investigate, by incoherent neutron scattering, the subnanosecond time scale dynamics of three model proteins: the mesophilic lysozyme, the thermophilic thermolysin, and the intrinsically disordered β-casein. Moreover, we address the influence of water, glycerol, and glucose, which create progressively more viscous matrices around the protein surface. By comparing the protein thermal fluctuations, we find that the internal dynamics of thermolysin are less affected by the environment compared to lysozyme and β-casein. We ascribe this behavior to the protein dynamic personality, i.e., to the stiffer dynamics of the thermophilic protein that contrasts the influence of the environment. Remarkably, lysozyme and thermolysin in all molecular environments reach a critical common flexibility when approaching the calorimetric melting temperature.

Atomistic simulations of RNA duplex thermal denaturation: Sequence- and forcefield-dependence

Double-stranded RNA is the end-product of template-based replication, and is also the functional state of some biological RNAs. Similarly to proteins and DNA, they can be denatured by temperature, with important physiological and technological implications. Here, we use an in silico strategy to probe the thermal denaturation of RNA duplexes. Following previous results that were obtained on a few different duplexes, and which nuanced the canonical 2-state picture of nucleic acid denaturation, we here specifically address three different aspects that greatly improve our description of the temperature-induced dsRNA separation. First, we investigate the effect of the spatial distribution of weak and strong base-pairs among the duplex sequence. We show that the deviations from the two-state dehybridization mechanism are more pronounced when a strong core is flanked with weak extremities, while duplexes with a weak core but strong extremities exhibit a two-state behavior, which can be explained by the key role played by base fraying. This was later verified by generating artificial hairpin or circular states containing one or two locked duplex extremities, which results in an important reinforcement of the entire HB structure of the duplex and higher melting temperatures. Finally, we demonstrate that our results are little sensitive to the employed combination of RNA and water forcefields. The trends in thermal stability among the different sequences as well as the observed unfolding mechanisms (and the deviations from a two-state scenario) remain the same regardless of the employed atomistic models. However, our study points to possible limitations of recent reparametrizations of the Amber RNA forcefield, which sometimes results in duplexes that readily denature under ambient conditions, in contradiction with available experimental results.

Decoding the Role of the Global Proteome Dynamics for Cellular Thermal Stability

Molecular mechanisms underlying the thermal response of cells remain elusive. On the basis of the recent result that the short-time diffusive dynamics of the Escherichia coli proteome is an excellent indicator of temperature-dependent bacterial metabolism and death, we used neutron scattering (NS) spectroscopy and molecular dynamics (MD) simulations to investigate the sub-nanosecond proteome mobility in psychro-, meso-, and hyperthermophilic bacteria over a wide temperature range. The magnitude of thermal fluctuations, measured by atomic mean square displacements, is similar among all studied bacteria at their respective thermal cell death. Global roto-translational motions turn out to be the main factor distinguishing the bacterial dynamical properties. We ascribe this behavior to the difference in the average proteome net charge, which becomes less negative for increasing bacterial thermal stability. We propose that the chemical-physical properties of the cytoplasm and the global dynamics of the resulting proteome are fine-tuned by evolution to uphold optimal thermal stability conditions.

Molecular dynamics simulations reveal the hidden EF-hand of EF-SAM as a possible key thermal sensor for STIM1 activation by temperature

Intracellular calcium signaling is essential for many cellular processes, including store-operated Ca2+ entry (SOCE), which is initiated by stromal interaction molecule 1 (STIM1) detecting endoplasmic reticulum (ER) Ca2+ depletion. STIM1 is also activated by temperature independent of ER Ca2+ depletion. Here we provide evidence, from advanced molecular dynamics simulations, that EF-SAM may act as a true temperature sensor for STIM1, with the prompt and extended unfolding of the hidden EF-hand subdomain (hEF) even at slightly elevated temperatures, exposing a highly conserved hydrophobic Phe108. Our study also suggests an interplay between Ca2+ and temperature sensing, as both, the canonical EF-hand subdomain (cEF) and the hidden EF-hand subdomain (hEF), exhibit much higher thermal stability in the Ca2+-loaded form compared to the Ca2+-free form. The SAM domain, surprisingly, displays high thermal stability compared to the EF-hands and may act as a stabilizer for the latter. We propose a modular architecture for the EF-hand-SAM domain of STIM1 composed of a thermal sensor (hEF), a Ca2+ sensor (cEF), and a stabilizing domain (SAM). Our findings provide important insights into the mechanism of temperature-dependent regulation of STIM1, which has broad implications for understanding the role of temperature in cellular physiology.

Toward a Molecular Mechanism of Complementary RNA Duplexes Denaturation

RNA duplexes are relatively rare but play very important biological roles. As an end-product of template-based RNA replication, they also have key implications for hypothetical primitive forms of life. Unless they are specifically separated by enzymes, these duplexes denature upon a temperature increase. However, mechanistic and kinetic aspects of RNA (and DNA) duplex thermal denaturation remain unclear at the microscopic level. We propose an in silico strategy that probes the thermal denaturation of RNA duplexes and allows for an extensive conformational space exploration along a wide temperature range with atomistic precision. We show that this approach first accounts for the strong sequence and length dependence of the duplexes melting temperature, reproducing the trends seen in the experiments and predicted by nearest-neighbor models. The simulations are then instrumental at providing a molecular picture of the temperature-induced strand separation. The textbook canonical "all-or-nothing" two-state model, very much inspired by the protein folding mechanism, can be nuanced. We demonstrate that a temperature increase leads to significantly distorted but stable structures with extensive base-fraying at the extremities, and that the fully formed duplexes typically do not form around melting. The duplex separation therefore appears as much more gradual than commonly thought.

Microscopic versus Macroscopic Glass Transitions and Relevant Length Scales in Mixtures of Industrial Interest

We have combined X-ray diffraction, neutron diffraction with polarization analysis, small-angle neutron scattering (SANS), neutron elastic fixed window scans (EFWS), and differential scanning calorimetry (DSC) to investigate polymeric blends of industrial interest composed by isotopically labeled styrene-butadiene rubber (SBR) and polystyrene (PS) oligomers of size smaller than the Kuhn length. The EFWS are sensitive to the onset of liquid-like motions across the calorimetric glass transition, allowing the selective determination of the "microscopic" effective glass transitions of the components. These are compared with the "macroscopic" counterparts disentangled by the analysis of the DSC results in terms of a model based on the effects of thermally driven concentration fluctuations and self-concentration. At the microscopic level, the mixtures are dynamically heterogeneous for blends with intermediate concentrations or rich in PS, while the sample with highest content of the fast SBR component looks as dynamically homogeneous. Moreover, the combination of SANS and DSC has allowed determining the relevant length scale for the α-relaxation through its loss of equilibrium to be ≈30 Å. This is compared with the different characteristic length scales that can be identified in these complex mixtures from structural, thermodynamical, and dynamical points of view because of the combined approach followed. We also discuss the sources of the non-Gaussian effects observed for the atomic displacements and the applicability of a Lindemann-like criterion in these materials.

Polymorphism and Ligand Binding Modulate Fast Dynamics of Human Telomeric G-Quadruplexes

Telomeric G-quadruplexes (G4s) are promising targets in the design and development of anticancer drugs. Their actual topology depends on several factors, resulting in structural polymorphism. In this study, we investigate how the fast dynamics of the telomeric sequence AG3(TTAG3)3 (Tel22) depends on the conformation. By using Fourier transform Infrared spectroscopy, we show that, in the hydrated powder state, Tel22 adopts parallel and mixed antiparallel/parallel topologies in the presence of K+ and Na+ ions, respectively. These conformational differences are reflected in the reduced mobility of Tel22 in Na+ environment in the sub-nanosecond timescale, as probed by elastic incoherent neutron scattering. These findings are consistent with the G4 antiparallel conformation being more stable than the parallel one, possibly due to the presence of ordered hydration water networks. In addition, we study the effect of Tel22 complexation with BRACO19 ligand. Despite the quite similar conformation in the complexed and uncomplexed state, the fast dynamics of Tel22-BRACO19 is enhanced compared to that of Tel22 alone, independently of the ions. We ascribe this effect to the preferential binding of water molecules to Tel22 against the ligand. The present results suggest that the effect of polymorphism and complexation on the G4 fast dynamics is mediated by hydration water.

Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations

In this chapter, we describe a protocol to estimate the thermal stability of single domain antibodies (sdAbs) using molecular dynamics (MD) simulations. This method measures the Q-value, the fraction of the native contacts, along the trajectory of high-temperature MD simulations starting from the experimental X-ray structure. We show a good correlation between the Q-value and the experimental melting temperature (T_m) in seven sdAbs. Assessing the Q-value on a per-residue level enabled us to identify residues that contribute to the instability and thus demonstrate which residues could be mutated to improve the stability and have later been validated by experiments. Our protocol extends beyond the application on sdAbs, as it is also suitable for other proteins and to determine the interfacial stability between protein and ligand.

Role of fast dynamics in the complexation of G-quadruplexes with small molecules

G-quadruplexes (G4s) formed by the human telomeric sequence AG₃ (TTAG₃)₃ (Tel22) play a key role in cancer and aging. We combined elastic incoherent neutron scattering (EINS) and quasielastic incoherent neutron scattering (QENS) to characterize the internal dynamics of Tel22 G4s and to assess how it is affected by complexation with two standard ligands, Berberine and BRACO19. We show that the interaction with the two ligands induces an increase of the overall mobility of Tel22 as quantified by the mean squared displacements (MSD) of hydrogen atoms. At the same time, the complexes display a lower stiffness than G4 alone. Two different types of motion characterize the G4 nanosecond timescale dynamics. Upon complexation, an increasing fraction of G4 atomic groups participate in this fast dynamics, along with an increase in the relevant characteristic length scales. We suggest that the entropic contribution to the conformational free energy of these motions might be crucial for the complexation mechanisms.

Protein Dynamics to Define and Refine Disordered Protein Ensembles

Intrinsically disordered proteins and unfolded proteins have fluctuating conformational ensembles that are fundamental to their biological function and impact protein folding, stability, and misfolding. Despite the importance of protein dynamics and conformational sampling, time-dependent data types are not fully exploited when defining and refining disordered protein ensembles. Here we introduce a computational framework using an elastic network model and normal-mode displacements to generate a dynamic disordered ensemble consistent with NMR-derived dynamics parameters, including transverse R₂ relaxation rates and Lipari-Szabo order parameters (S² values). We illustrate our approach using the unfolded state of the drkN SH3 domain to show that the dynamical ensembles give better agreement than a static ensemble for a wide range of experimental validation data including NMR chemical shifts, J-couplings, nuclear Overhauser effects, paramagnetic relaxation enhancements, residual dipolar couplings, hydrodynamic radii, single-molecule fluorescence Förster resonance energy transfer, and small-angle X-ray scattering.

Computational Insights into the Unfolding of a Destabilized Superoxide Dismutase 1 Mutant

In this work, we investigate the β-barrel of superoxide dismutase 1 (SOD1) in a mutated form, the isoleucine 35 to alanine (I35A) mutant, commonly used as a model system to decipher the role of the full-length apoSOD1 protein in amyotrophic lateral sclerosis (ALS). It is known from experiments that the mutation reduces the stability of the SOD1 barrel and makes it largely unfolded in the cell at 37 degrees Celsius. We deploy state-of-the-art computational machinery to examine the thermal destabilization of the I35A mutant by comparing two widely used force fields, Amber a99SB-disp and CHARMM36m. We find that only the latter force field, when combined with the Replica Exchange with Solute Scaling (REST2) approach, reproduces semi-quantitatively the experimentally observed shift in the melting between the original and the mutated SOD1 barrel. In addition, we analyze the unfolding process and the conformational landscape of the mutant, finding these largely similar to those of the wildtype. Nevertheless, we detect an increased presence of partially misfolded states at ambient temperatures. These states, featuring conformational changes in the region of the β-strands β4-β6, might provide a pathway for nonnative aggregation.

A Minireview on Temperature Dependent Protein Conformational Sampling

In this minireview we discuss the role of the more subtle conformational change-protein conformational sampling and connect it to the classic relationship of protein structure and function. The theory of pre-existing functional states of protein are discussed in context of alternate protein conformational sampling. Last, we discuss how temperature, ligand binding and mutations affect the protein conformational sampling mode which is linked to the protein function regulation. The review includes several protein systems that showed temperature dependent protein conformational sampling. We also specifically included two enzyme systems, thermophilic alcohol dehydrogenase (ht-ADH) and thermolysin which we previously studied when discussing temperature dependent protein conformational sampling.

Specific Interactions and Environment Flexibility Tune Protein Stability under Extreme Crowding

Macromolecular crowding influences protein mobility and stability in vivo. A precise description of the crowding effect on protein thermal stability requires the estimate of the combined effects of excluded volume, specific protein-environment interactions, as well as the thermal response of the crowders. Here, we explore an ideal model system, the lysozyme protein in powder state, to dissect the factors controlling the melting of the protein under extreme crowding. By deploying state-of-the art molecular simulations, supported by calorimetric experiments, we assess the role of the environment flexibility and of intermolecular electrostatic interactions. In particular, we show that the temperature-dependent flexibility of the macromolecular crowders, along with specific interactions, significantly alleviates the stabilizing contributions of the static volume effect.

The number of catalytic cycles in an enzyme's lifetime and why it matters to metabolic engineering

The continuous replacement of enzymes and other proteins appropriates up to half the maintenance energy budget in microorganisms and plants. High enzyme replacement rates therefore cut the productivity of biosystems ranging from microbial fermentations to crops. However, yardsticks to assess what drives enzyme protein replacement and guidelines on how to reduce it are lacking. Accordingly, we compared enzymes’ life spans across kingdoms using a new yardstick (catalytic cycles until replacement [CCR]) and related CCR to enzyme reaction chemistry. We concluded that 1) many enzymes fail due to collateral damage from the reaction they catalyze, and 2) such damage and its attendant enzyme replacement costs are mitigable by engineering and are therefore promising targets for synthetic biology.

Metabolic engineering uses enzymes as parts to build biosystems for specified tasks. Although a part’s working life and failure modes are key engineering performance indicators, this is not yet so in metabolic engineering because it is not known how long enzymes remain functional in vivo or whether cumulative deterioration (wear-out), sudden random failure, or other causes drive replacement. Consequently, enzymes cannot be engineered to extend life and cut the high energy costs of replacement. Guided by catalyst engineering, we adopted catalytic cycles until replacement (CCR) as a metric for enzyme functional life span in vivo. CCR is the number of catalytic cycles that an enzyme mediates in vivo before failure or replacement, i.e., metabolic flux rate/protein turnover rate. We used estimated fluxes and measured protein turnover rates to calculate CCRs for ∼100–200 enzymes each from Lactococcus lactis, yeast, and Arabidopsis. CCRs in these organisms had similar ranges (<10³ to >10⁷) but different median values (3–4 × 10⁴ in L. lactis and yeast versus 4 × 10⁵ in Arabidopsis). In all organisms, enzymes whose substrates, products, or mechanisms can attack reactive amino acid residues had significantly lower median CCR values than other enzymes. Taken with literature on mechanism-based inactivation, the latter finding supports the proposal that 1) random active-site damage by reaction chemistry is an important cause of enzyme failure, and 2) reactive noncatalytic residues in the active-site region are likely contributors to damage susceptibility. Enzyme engineering to raise CCRs and lower replacement costs may thus be both beneficial and feasible.

Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins

Many pairwise additive force fields are in active use for intrinsically disordered proteins (IDPs) and regions (IDRs), some of which modify energetic terms to improve the description of IDPs/IDRs but are largely in disagreement with solution experiments for the disordered states. This work considers a new direction-the connection to configurational entropy-and how it might change the nature of our understanding of protein force field development to equally well encompass globular proteins, IDRs/IDPs, and disorder-to-order transitions. We have evaluated representative pairwise and many-body protein and water force fields against experimental data on representative IDPs and IDRs, a peptide that undergoes a disorder-to-order transition, for seven globular proteins ranging in size from 130 to 266 amino acids. We find that force fields with the largest statistical fluctuations consistent with the radius of gyration and universal Lindemann values for folded states simultaneously better describe IDPs and IDRs and disorder-to-order transitions. Hence, the crux of what a force field should exhibit to well describe IDRs/IDPs is not just the balance between protein and water energetics but the balance between energetic effects and configurational entropy of folded states of globular proteins.

Kinetics of Network Formation and Heterogeneous Dynamics of an Egg White Gel Revealed by Coherent X-Ray Scattering

The kinetics of heat-induced gelation and the microscopic dynamics of a hen egg white gel are probed using x-ray photon correlation spectroscopy along with ultrasmall-angle x-ray scattering. The kinetics of structural growth reveals a reaction-limited aggregation process with a gel fractal dimension of ≈2 and an average network mesh size of ca. 400 nm. The dynamics probed at these length scales reveals an exponential growth of the characteristic relaxation times followed by an intriguing steady state in combination with a compressed exponential correlation function and a temporal heterogeneity. The degree of heterogeneity increases with decreasing length scale. We discuss our results in the broader context of experiments and models describing attractive colloidal gels.

Atomic scale investigation of the volume phase transition in concentrated PNIPAM microgels

Combining elastic incoherent neutron scattering and differential scanning calorimetry, we investigate the occurrence of the volume phase transition (VPT) in very concentrated poly-(N-isopropyl-acrylamide) (PNIPAM) microgel suspensions, from a polymer weight fraction of 30 wt. % up to dry conditions. Although samples are arrested at the macroscopic scale, atomic degrees of freedom are equilibrated and can be probed in a reproducible way. A clear signature of the VPT is present as a sharp drop in the mean square displacement of PNIPAM hydrogen atoms obtained by neutron scattering. As a function of concentration, the VPT gets smoother as dry conditions are approached, whereas the VPT temperature shows a minimum at about 43 wt. %. This behavior is qualitatively confirmed by calorimetry measurements. Molecular dynamics simulations are employed to complement experimental results and gain further insights into the nature of the VPT, confirming that it involves the formation of an attractive gel state between the microgels. Overall, these results provide evidence that the VPT in PNIPAM-based systems can be detected at different time- and length-scales as well as under overcrowded conditions.

The Unfolding Journey of Superoxide Dismutase 1 Barrels under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions with Crowders

The thermal stability of the superoxide dismutase 1 protein in a crowded solution is investigated by performing enhanced sampling molecular simulations. By complementing thermal unfolding experiments done close to physiological conditions (200 mg/mL), we provide evidence that the presence of the protein crowder bovine serum albumin in different packing states has only a minor, and essentially destabilizing, effect. The finding that quinary interactions counteract the pure stabilization contribution stemming from excluded volume is rationalized here by exploring the SOD1 unfolding mechanism in microscopic detail. In agreement with recent experiments, we unveil the importance of intermediate unfolded states as well as the correlation between protein conformations and local packing with the crowders. This link helps us to elucidate why certain SOD1 mutations involved in the ALS disease reverse the stability effect of the intracellular environment.

Rapid Characterization of Biomolecules' Thermal Stability in a Segmented Flow-Through Optofluidic Microsystem

Optofluidic devices combining optics and microfluidics have recently attracted attention for biomolecular analysis due to their high detection sensitivity. Here, we show a silicon chip with tubular microchannels buried inside the substrate featuring temperature gradient (∇T) along the microchannel. We set up an optical fluorescence system consisting of a power-modulated laser light source of 470 nm coupled to the microchannel serving as a light guide via optical fiber. Fluorescence was detected on the other side of the microchannel using a photomultiplier tube connected to an optical fiber via a fluorescein isothiocyanate filter. The PMT output was connected to a lock-in amplifier for signal processing. We performed a melting curve analysis of a short dsDNA - SYBR Green I complex with a known melting temperature (TM) in a flow-through configuration without gradient to verify the functionality of the proposed detection system. We then used the segmented flow configuration and measured the fluorescence amplitude of a droplet exposed to ∇T of ≈ 2.31 °C mm-1, determining the heat transfer time as ≈ 554 ms. The proposed platform can be used as a fast and cost-effective system for performing either MCA of dsDNAs or for measuring protein unfolding for drug-screening applications.

Protein thermal stability

Proteins, in general, fold to a well-organized three-dimensional structure in order to function. The stability of this functional shape can be perturbed by external environmental conditions, such as temperature. Understanding the molecular factors underlying the resistance of proteins to the thermal stress has important consequences. First of all, it can aid the design of thermostable enzymes able to perform efficient catalysis in the high-temperature regime. Second, it is an essential brick of knowledge required to decipher the evolutionary pathways of life adaptation on Earth. Thanks to the development of atomistic simulations and ad hoc enhanced sampling techniques, it is now possible to investigate this problem in silico, and therefore provide support to experiments. After having described the methodological aspects, the chapter proposes an extended discussion on two problems. First, we focus on thermophilic proteins, a perfect model to address the issue of thermal stability and molecular evolution. Second, we discuss the issue of how protein thermal stability is affected by crowded in vivo-like conditions.

Order–disorder skewness in alpha-synuclein: a key mechanism to recognize membrane curvature

Currently, membrane curvature is understood as an active mechanism to control cells spatial organization and activity.

Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes

The thermal resistance of two homolog enzymes is investigated, with an emphasis on their local stability and flexibility, and on the possible implications regarding their reactivity.

Disentangling time-focusing from beam divergence: A novel approach for high-flux thermal neutron spectroscopy at continuous and long-pulse sources

We present the concept of a novel time-focusing technique for neutron spectrometers, which allows us to disentangle time-focusing from beam divergence. The core of this approach is a double rotating-crystal monochromator that can be used to extract a larger wavelength band from a white beam, thus providing a higher flux at the sample compared to standard time-of-flight instruments, yet preserving energy resolution and beam collimation. The performances of a spectrometer based on this approach are quantitatively discussed in terms of possible incident wavelengths, flux at the sample, and (Q, E)-resolution. Analytical estimates suggest flux gains of about one order of magnitude at comparable resolutions in comparison to conventional time-of-flight spectrometers. Moreover, the double monochromator configuration natively shifts the sample away from the source line-of-sight, thus significantly improving the signal-to-noise ratio. The latter, in combination with a system that does not increase the beam divergence, brings the further advantage of a cleaner access to the low-Q region, which is recognized to be of fundamental interest for magnetism and for disordered materials, from glasses to biological systems.

Effect of aqueous medium on low-frequency dynamics, chemical activity and physical properties of a spherical virus

In this work, we have studied the effect of size and aqueous medium on the low-frequency dynamics, physical properties like melting temperature and glass transition temperature and chemical properties like catalytic activation energy of spherical virus using Lindemann's criteria and Arrhenius relation under their dynamic limit. The melting temperature and catalytic activation energy decrease with decreasing size of spherical virus. The glass transition temperature which increases with decreasing size of the virus is analyzed through the size dependent melting temperature. The melting temperature and catalytic activation energy of spherical virus of particular size increases when it is embedded in glycerol or water due to mismatch of the physical properties at the interface of virus and surrounding medium. In addition, the glass transition temperature of free and glycerol/water embedded virus using low-frequency vibrational modes has been calculated under the framework of elastic continuum approximation model. The glass transition temperature of spherical virus decreases with size when embedded in glycerol or water. A correlation between [Formula: see text] and [Formula: see text] is also drawn for spherical viruses. The study can be useful for spherical virus borne therapy i.e. in detecting and killing of the spherical viruses using a principle based on acoustic phonons (sound waves) resonance.Communicated by Ramaswamy H. Sarma.

Thermal stability of single-domain antibodies estimated by molecular dynamics simulations

Single‐domain antibodies (sdAbs) function like regular antibodies, however, consist of only one domain. Because of their low molecular weight, sdAbs have advantages with respect to production and delivery to their targets and for applications such as antibody drugs and biosensors. Thus, sdAbs with high thermal stability are required. In this work, we chose seven sdAbs, which have a wide range of melting temperature (T_m) values and known structures. We applied molecular dynamics (MD) simulations to estimate their relative stability and compared them with the experimental data. High‐temperature MD simulations at 400 K and 500 K were executed with simulations at 300 K as a control. The fraction of native atomic contacts, Q, measured for the 400 K simulations showed a fairly good correlation with the T_m values. Interestingly, when the residues were classified by their hydrophobicity and size, the Q values of hydrophilic residues exhibited an even better correlation, suggesting that stabilization is correlated with favorable interactions of hydrophilic residues. Measuring the Q value on a per‐residue level enabled us to identify residues that contribute significantly to the instability and thus demonstrating how our analysis can be used in a mutant case study.

Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins

Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scattering methods. These displacements can also be calculated numerically using data from molecular dynamics simulations. An enormous amount of data on the average mean-square motional displacement (MSD) of H as a function of protein temperature, hydration, and other conditions has been collected. H resides in a wide spectrum of sites in a protein. Some H are tightly bound to molecular chains, and the H motion is dictated by that of the chain. Other H are quite independent. As a result, there is a distribution of motions and MSDs of H within a protein that is denoted dynamical heterogeneity. The goal of this paper is to incorporate a distribution of MSDs into models of the H incoherent intermediate scattering function, I(Q,t), that is calculated and observed. The aim is to contribute information on the distribution as well as on the average MSD from comparison of the models with simulations and experiment. For example, we find that simulations of I(Q,t) in lysozyme are well reproduced if the distribution of MSDs is bimodal with two broad peaks rather than a single broad peak.

Mechanics of Protein Adaptation to High Temperatures

Inspired by Somero's corresponding state principle that relates protein enhanced thermal stability with mechanical rigidity, we deployed state of the art computational techniques (based on atomistic steered molecular dynamics and Hamiltonian-replica exchange simulations) to study the in silico realization of mechanical and thermal unfolding of two homologous Csp proteins that have evolved to thrive in different thermal environments. By complementing recent single-molecule experiments, we unambiguously show that, for these homologues whose structures are very similar, the increased thermal resistance of the thermophilic variant is not associated with an increased mechanical stability. Our approach provides microscopic insights that are otherwise inaccessible to experimental techniques, and explains why the protein weak spots for thermal and mechanical denaturation are distinct.