The heat capacity of proteins

G-quadruplexes catalyze protein folding by reshaping the energetic landscape

Many proteins have slow folding times in vitro that are physiologically untenable. To combat this challenge, ATP-dependent chaperonins are thought to possess the unique ability to catalyze protein folding. Performing quantitative model selection using protein folding and unfolding data, we here show that short nucleic acids containing G-quadruplex (G4) structure can also catalyze protein folding. Performing the experiments as a function of temperature demonstrates that the G4 reshapes the underlying driving forces of protein folding. As short nucleic acids can catalyze protein folding without the input of ATP, the ability of the cell to fold proteins is far higher than previously anticipated.

Investigation of Transient Temperature Rising of Light-Harvesting Complex II by Nonradiative Heat Dissipation at the Protein Level

Light-harvesting complex II (LHCII), the most abundant membrane protein in photosystem II, plays dual roles, i.e., efficient light harvesting and energy transfer to the reaction center under low light conditions and dissipating excess energy as heat to prevent photodamage under high irradiation conditions. The latter process is known as nonphotochemical quenching (NPQ). It has been established that both the pH gradient and temperature rise can trigger NPQ, while the transient heat release via nonradiative decay of the excess energy, as well as the accompanying transient temperature rising of LHCII at room temperature, have not been observed yet. Here we conducted femtosecond and nanosecond time-resolved visible pump and mid-infrared probe measurements on the LHCII trimer, respectively. We detected an excited-state heat dissipation-induced transient temperature rise in the LHCII trimer. The results show that the LHCII gets thermal equilibrium with D2O medium with a temperature rise of 7 °C under 480 nm excitation (mainly absorbed by Chlb and carotenoid) at a power of 0.4 mJ and a pulse duration of 10 ns, fairly consistent with the theoretical estimation of a temperature increase of 9.3 °C. Furthermore, we observed the conformational changes of LHCII in response to the raised temperature, i.e., from 310-helix/random coil to α-helix. Combining the femtosecond time-resolved visible pump and mid-infrared probe spectra, the light-induced temperature jump of LHCII is determined to take place around 60 ns.

Unusual Hydrophobic Property of Blue Fluorescent Amino Acid 4-Cyanotryptophan

It is a common belief that the negative heat capacity change (ΔCp) associated with protein folding, which is a manifestation of the hydrophobic effect, results from a decrease in the solvent accessible hydrophobic surface area. Herein, we investigate the conformational energy landscape and dynamics of a tetrapeptide composed of two glycine and two 4-cyanotryptophan residues using time-resolved fluorescence spectroscopy, molecular dynamics simulations, and density functional theory calculations and find that, contrary to this expectation, the hydrophobic association of two 4-cyanotryptophan side chains leads to a positive ΔCp (approximately 543 J K-1 mol-1). Furthermore, we find that promoting one of the 4-cyanotryptophans to its excited electronic state strengthens this self-association. Taken together, our results provide not only insight into how modification of an aromatic amino acid can affect its hydrophobicity but also a potential strategy for designing protein sequences that can fold (unfold) at high (low) temperatures.

Unravelling the stabilization mechanism of mono-, di- and tri-cholinium citrate-ethylene glycol DESs towards α-chymotrypsin for preservation and activation of the enzyme

Deep eutectic solvents (DESs) are considered as designer solvents that serve as alternatives to traditional solvents. Numerous favourable properties and advantageous characteristics promote their utility in bio-catalysis. Therefore, they have emerged as attractive sustainable media for different biomacromolecules. In the present work, we have synthesized cholinium-based DESs having a hydrogen bond acceptor (HBA) : hydrogen bond donor (HBD) molar ratio of 1 : 2 by varying the cationic ratio in the HBA, which led to the formation of the DESs such as monocholinium citrate ([Chn][Cit]), dicholinium citrate ([Chn]2[Cit]) and tricholinium citrate ([Chn]3[Cit]), keeping the HBD ethylene glycol (EG) constant to study their suitability for α-chymotrypsin (α-CT). Herein, we have systematically evaluated the influence of DES-1 ([Chn][Cit]-[EG]), DES-2 ([Chn]2[Cit]-[EG]) and DES-3 ([Chn]3[Cit]-[EG]) on the structural and thermal stability, thermodynamic profile, colloidal stability and enzymatic activity of α-CT using different spectroscopic techniques. The spectroscopic results explicitly show enhanced structural stability and activity of the enzyme as the cationic ratio in the HBA increases. Fascinatingly, temperature-dependent studies through both fluorescence and activity measurements showed that DES-2 and DES-3 have highly beneficial effects on α-CT stability. The transition temperature (Tm) of α-CT was augmented by 12.0 °C in DES-2, 10.0 °C in DES-3 and 9.1 °C in DES-1 when compared to the enzyme in buffer. Furthermore, transmission electron microscopy (TEM) analysis revealed that the morphology of α-CT in DES-2 and DES-3 closely mirrored the structure of α-CT, while DES-1 exhibited only minor structural deviations. These findings were corroborated by hydrodynamic size (dH) measurements and average decay time analysis, which confirmed the observed morphological similarities and perturbations. The long-term preservation ability and kinetics of DES-3 were eventually confirmed by Michaelis-Menten kinetics. Ultimately, these outcomes demonstrate that increasing the molar ratio of the cholinium cation in the HBA can enhance the ability of DESs to stabilize the α-CT structure. Our results also suggest that the effect imparted by DESs was due to DESs themselves rather than their constituent elements. Altogether, the present investigation provides a new insight into the dependence of protein's stability and conformational alterations on DES composition. Also, the biocompatibility of DESs towards enzymes can be varied by changing the molar ratios of the constituent components of DESs to facilitate the expansion of applicability of DESs in biocatalysis.

Modeling collisional kinetic energy damping, heating, and cooling of ions in mass spectrometers: a tutorial perspective

Many powerful methods in mass spectrometry rely on activation of ions by high-energy collisions with gas particles. For example, multiple Collision Induced Dissociation (CID) has been used for many years to determine structural information for ions ranging from small organics to large, native-like protein complexes. More recently, Collision Induced Unfolding (CIU) has proved to be a very powerful method for understanding high-order protein structure and detecting differences between similar proteins. Quantifying the thermochemistry underlying dissociation/unfolding in these experiments can be quite challenging without reliable models of ion heating and cooling. Established physical models of CID are valuable in predicting ion heating but do not explicitly include mechanisms for cooling, which may play a large part in CID/CIU in modern instruments. Ab initio and Molecular Dynamics methods are extremely computationally expensive for modeling CID/CIU of large analytes such as biomolecular ions. In this tutorial perspective, limiting behaviors of ion kinetic energy damping, heating, and cooling set by "extreme" cases are explored, and an Improved Impulsive Collision Theory and associated software ("Ion Simulations of the Physics of Activation", IonSPA) are introduced that can model all of these for partially inelastic collisions. Finally, examples of modeled collisional activation of native-like protein ions under realistic experimental conditions are discussed, with an outlook toward the use of IonSPA in accessing the thermochemical information hidden in CID breakdown curves and CIU fingerprints.

Thermal Energy Transport through Nonbonded Native Contacts in Protein

Within the protein interior, where we observe various types of interactions, nonuniform flow of thermal energy occurs along the polypeptide chain and through nonbonded native contacts, leading to inhomogeneous transport efficiencies from one site to another. The folded native protein serves not merely as thermal transfer medium but, more importantly, as sophisticated molecular nanomachines in cells. Therefore, we are particularly interested in what sort of "communication" is mediated through native contacts in the folded proteins and how such features are quantitatively depicted in terms of local transport coefficients of heat currents. To address the issue, we introduced a concept of inter-residue thermal conductivity and characterized the nonuniform thermal transport properties of a small globular protein, HP36, using equilibrium molecular dynamics simulation and the Green-Kubo formula. We observed that the thermal transport of the protein was dominated by that along the polypeptide chain, while the local thermal conductivity of nonbonded native contacts decreased in the order of H-bonding > π-stacking > electrostatic > hydrophobic contacts. Furthermore, we applied machine learning techniques to analyze the molecular mechanism of protein thermal transport. As a result, the contact distance, variance in contact distance, and H-bonding occurrence probability during MD simulations are found to be the top three important determinants for predicting local thermal transport coefficients.

A finely balanced order-disorder equilibrium sculpts the folding-binding landscape of an antibiotic sequestering protein

TipA, a MerR family transcription factor from Streptomyces lividans, promotes antibiotic resistance by sequestering broad-spectrum thiopeptide-based antibiotics, thus counteracting their inhibitory effect on ribosomes. TipAS, a minimal binding motif which is expressed as an isoform of TipA, harbors a partially disordered N-terminal subdomain that folds upon binding multiple antibiotics. The extent and nature of the underlying molecular heterogeneity in TipAS that shapes its promiscuous folding-function landscape is an open question and is critical for understanding antibiotic-sequestration mechanisms. Here, combining equilibrium and time-resolved experiments, statistical modeling, and simulations, we show that the TipAS native ensemble exhibits a pre-equilibrium between binding-incompetent and binding-competent substates, with the fully folded state appearing only as an excited state under physiological conditions. The binding-competent state characterized by a partially structured N-terminal subdomain loses structure progressively in the physiological range of temperatures, swells on temperature increase, and displays slow conformational exchange across multiple conformations. Binding to the bactericidal antibiotic thiostrepton follows a combination of induced-fit and conformational-selection-like mechanisms, via partial binding and concomitant stabilization of the binding-competent substate. These ensemble features are evolutionarily conserved across orthologs from select bacteria that infect humans, underscoring the functional role of partial disorder in the native ensemble of antibiotic-sequestering proteins belonging to the MerR family.

Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable

Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.

Direct Determination of High-Affinity Binding Constants by Continuous Injection Isothermal Titration Calorimetry

Isothermal titration calorimetry (ITC) is a method to determine thermodynamic values (ΔG, ΔH, and ΔS) for ligand-receptor binding in biological and abiological systems. It is challenging to directly determine subnanomolar dissociation constants using a standard incremental injection approach ITC (IIA-ITC) measurement. We recently demonstrated a continuous injection approach ITC (CIA-ITC) [ J. Phys. Chem. B 2021, 125, 8075-8087]enables the estimation of thermodynamic parameters in situ. In this work, we demonstrate a label-free and surface modification-free CIA-ITC to determine the complete binding thermodynamics of a ligand with a subnanomolar dissociation constant KD. The KD for desthiobiotin (DTB)-avidin binding was determined to be 6.5 pM with respect to the ligand by CIA-ITC, a quantity unsuccessfully measured with IIA-ITC and surface plasmon resonance spectroscopy (SPR). This value compares well with literature-reported spectroscopic determination of DTB-avidin binding. Criteria with respect to the concentration of the ligand and receptor and flow rate for obtaining true equilibrium dissociation constants without displacement titration are presented.

Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in Paralogous Plasmodium Acyl-CoA Binding Proteins

Paralogous proteins confer enhanced fitness to organisms via complex sequence-conformation codes that shape functional divergence, specialization, or promiscuity. Here, we dissect the underlying mechanism of promiscuous binding versus partial subfunctionalization in paralogues by studying structurally identical acyl-CoA binding proteins (ACBPs) from Plasmodium falciparum that serve as promising drug targets due to their high expression during the protozoan proliferative phase. Combining spectroscopic measurements, solution NMR, SPR, and simulations on two of the paralogues, A16 and A749, we show that minor sequence differences shape nearly every local and global conformational feature. A749 displays a broader and heterogeneous native ensemble, weaker thermodynamic coupling and cooperativity, enhanced fluctuations, and a larger binding pocket volume compared to A16. Site-specific tryptophan probes signal a graded reduction in the sampling of substates in the holo form, which is particularly apparent in A749. The paralogues exhibit a spectrum of binding affinities to different acyl-CoAs with A749, the more promiscuous and hence the likely ancestor, binding 1000-fold stronger to lauroyl-CoA under physiological conditions. We thus demonstrate how minor sequence changes modulate the extent of long-range interactions and dynamics, effectively contributing to the molecular evolution of contrasting functional repertoires in paralogues.

Thermal transport across membranes and the Kapitza length from photothermal microscopy

An analytical model is presented for light scattering associated with heat transport near a cell membrane that divides a complex system into two topologically distinct half-spaces. Our analysis is motivated by experiments on vibrational photothermal microscopy which have not only demonstrated remarkably high contrast and resolution, but also are capable of providing label-free local information of heat transport in complex morphologies. In the first Born approximation, the derived Green's function leads to the reconstruction of a full 3D image with photothermal contrast obtained using both amplitude and phase detection of periodic excitations. We show that important fundamental parameters including the Kapitza length and Kapitza resistance can be derived from experiments. Our goal is to spur additional experimental studies with high-frequency modulation and heterodyne detection in order to make contact with recent theoretical molecular dynamics calculations of thermal transport properties in membrane systems.

Energy Landscapes and Heat Capacity Signatures for Monomers and Dimers of Amyloid-Forming Hexapeptides

Amyloid formation is a hallmark of various neurodegenerative disorders. In this contribution, energy landscapes are explored for various hexapeptides that are known to form amyloids. Heat capacity (CV) analysis at low temperature for these hexapeptides reveals that the low energy structures contributing to the first heat capacity feature above a threshold temperature exhibit a variety of backbone conformations for amyloid-forming monomers. The corresponding control sequences do not exhibit such structural polymorphism, as diagnosed via end-to-end distance and a dihedral angle defined for the monomer. A similar heat capacity analysis for dimer conformations obtained using basin-hopping global optimisation shows clear features in end-to-end distance versus dihedral correlation plots, where amyloid-forming sequences exhibit a preference for larger end-to-end distances and larger positive dihedrals. These results hold true for sequences taken from tau, amylin, insulin A chain, a de novo designed peptide, and various control sequences. While there is a little overall correlation between the aggregation propensity and the temperature at which the low-temperature CV feature occurs, further analysis suggests that the amyloid-forming sequences exhibit the key CV feature at a lower temperature compared to control sequences derived from the same protein.

Implications of a temperature-dependent heat capacity for temperature-gated ion channels

Temperature influences dynamics and state-equilibrium distributions in all molecular processes, and only a relatively narrow range of temperatures is compatible with life-organisms must avoid temperature extremes that can cause physical damage or metabolic disruption. Animals evolved a set of sensory ion channels, many of them in the family of transient receptor potential cation channels that detect biologically relevant changes in temperature with remarkable sensitivity. Depending on the specific ion channel, heating or cooling elicits conformational changes in the channel to enable the flow of cations into sensory neurons, giving rise to electrical signaling and sensory perception. The molecular mechanisms responsible for the heightened temperature-sensitivity in these ion channels, as well as the molecular adaptations that make each channel specifically heat- or cold-activated, are largely unknown. It has been hypothesized that a heat capacity difference (ΔCp) between two conformational states of these biological thermosensors can drive their temperature-sensitivity, but no experimental measurements of ΔCp have been achieved for these channel proteins. Contrary to the general assumption that the ΔCp is constant, measurements from soluble proteins indicate that the ΔCp is likely to be a function of temperature. By investigating the theoretical consequences for a linearly temperature-dependent ΔCp on the open-closed equilibrium of an ion channel, we uncover a range of possible channel behaviors that are consistent with experimental measurements of channel activity and that extend beyond what had been generally assumed to be possible for a simple two-state model, challenging long-held assumptions about ion channel gating models at equilibrium.

Measurement of cellular thermal properties and their temperature dependence based on frequency spectra via an on-chip-integrated microthermistor

To understand the mechanism of intracellular thermal transport, thermal properties must be elucidated, particularly thermal conductivity and specific heat capacity. However, these properties have not been extensively studied. In this study, we developed a cellular temperature measurement device with a high temperature resolution of 1.17 m °C under wet conditions and with the ability to introduce intracellular local heating using a focused infrared laser to cultured cells on the device surface. Using this device, we evaluated the thermal properties of single cells based on their temperature signals and responses. Measurements were taken using on-chip-integrated microthermistors with high temperature resolution at varying surrounding temperatures and frequencies of local infrared irradiation on cells prepared on the sensors. Frequency spectra were used to determine the intensities of the temperature signals with respect to heating times. Signal intensities at 37 °C and a frequency lower than 2 Hz were larger than those at 25 °C, which were similar to those of water. The apparent thermal conductivity and specific heat capacity, which were determined at different surrounding temperatures and local heating frequencies, were lower than and similar to those of water at 37 °C and 25 °C, respectively. Our results indicate that the thermal properties of cells depend on both temperatures and physiological activities in addition to local heating frequencies.

Protein Stability─Analysis of Heat and Cold Denaturation without and with Unfolding Models

Protein stability is important in many areas of life sciences. Thermal protein unfolding is investigated extensively with various spectroscopic techniques. The extraction of thermodynamic properties from these measurements requires the application of models. Differential scanning calorimetry (DSC) is less common, but is unique as it measures directly a thermodynamic property, that is, the heat capacity C_p(T). The analysis of C_p(T) is usually performed with the chemical equilibrium two-state model. This is not necessary and leads to incorrect thermodynamic consequences. Here we demonstrate a straightforward model-independent evaluation of heat capacity experiments in terms of protein unfolding enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T)). This now allows the comparison of the experimental thermodynamic data with the predictions of different models. We critically examined the standard chemical equilibrium two-state model, which predicts a positive free energy for the native protein, and diverges distinctly from the experimental temperature profiles. We propose two new models which are equally applicable to spectroscopy and calorimetry. The Θ_U(T)-weighted chemical equilibrium model and the statistical-mechanical two-state model provide excellent fits of the experimental data. They predict sigmoidal temperature profiles for enthalpy and entropy, and a trapezoidal temperature profile for the free energy. This is illustrated with experimental examples for heat and cold denaturation of lysozyme and β-lactoglobulin. We then show that the free energy is not a good criterion to judge protein stability. More useful parameters are discussed, including protein cooperativity. The new parameters are embedded in a well-defined thermodynamic context and are amenable to molecular dynamics calculations.

Protein Unfolding-Thermodynamic Perspectives and Unfolding Models

We review the key steps leading to an improved analysis of thermal protein unfolding. Thermal unfolding is a dynamic cooperative process with many short-lived intermediates. Protein unfolding has been measured by various spectroscopic techniques that reveal structural changes, and by differential scanning calorimetry (DSC) that provides the heat capacity change Cp(T). The corresponding temperature profiles of enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T) have thus far been evaluated using a chemical equilibrium two-state model. Taking a different approach, we demonstrated that the temperature profiles of enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T) can be obtained directly by a numerical integration of the heat capacity profile Cp(T). DSC thus offers the unique possibility to assess these parameters without resorting to a model. These experimental parameters now allow us to examine the predictions of different unfolding models. The standard two-state model fits the experimental heat capacity peak quite well. However, neither the enthalpy nor entropy profiles (predicted to be almost linear) are congruent with the measured sigmoidal temperature profiles, nor is the parabolic free energy profile congruent with the experimentally observed trapezoidal temperature profile. We introduce three new models, an empirical two-state model, a statistical-mechanical two-state model and a cooperative statistical-mechanical multistate model. The empirical model partially corrects for the deficits of the standard model. However, only the two statistical-mechanical models are thermodynamically consistent. The two-state models yield good fits for the enthalpy, entropy and free energy of unfolding of small proteins. The cooperative statistical-mechanical multistate model yields perfect fits, even for the unfolding of large proteins such as antibodies.

Intrinsic affinity of protein - ligand binding by differential scanning calorimetry

Differential scanning calorimetry (DSC) determines the enthalpy change upon protein unfolding and the melting temperature of the protein. Performing DSC of a protein in the presence of increasing concentrations of specifically-binding ligand yields a series of curves that can be fit to obtain the protein-ligand dissociation constant as done in the fluorescence-based thermal shift assay (FTSA, ThermoFluor, DSF). The enthalpy of unfolding, as directly determined by DSC, helps improving the precision of the fit. If the ligand binding is linked to protonation reactions, the intrinsic binding constant can be determined by performing the affinity determination at a series of pH values. Here, the intrinsic, pH-independent, affinity of acetazolamide binding to carbonic anhydrase (CA) II was determined. A series of high-affinity ligands binding to CAIX, an anticancer drug target, and CAII showed recognition and selectivity for the anticancer isozyme. Performing the DSC experiment in buffers of highly different enthalpies of protonation enabled to observe the ligand unbinding-linked protonation reactions and estimate the intrinsic enthalpy of binding. The heat capacity of combined unfolding and unbinding was determined by varying the ligand concentrations. Taken together, these parameters provided a detailed thermodynamic picture of the linked ligand binding and protein unfolding process.

Structural and ITC Characterization of Peptide-Protein Binding: Thermodynamic Consequences of Cyclization Constraints, a Case Study on Vascular Endothelial Growth Factor Ligands

Macrocyclization constraints are widely used in the design of protein ligands to stabilize their bioactive conformation and increase their affinities. However, the resulting changes in binding entropy can be puzzling and uncorrelated to affinity gains. Here, the thermodynamic (Isothermal Titration Calorimetry) and structural (X-ray, NMR and CD) analysis of a complete series of lactam-bridged peptide ligands of the vascular endothelial growth factor, and their unconstrained analogs are reported. It is shown that differences in thermodynamics arise mainly from the folding energy of the peptide upon binding. The systematic reduction in conformational entropy penalty due to helix pre-organization can be counterbalanced by an unfavorable vibrational entropy change if the constraints are too rigid. The gain in configurational entropy partially escapes the enthalpy/entropy compensation and leads to an improvement in affinity. The precision of the analytical ITC method makes this study a possible benchmark for constrained peptides optimization.

Altered Conformational Landscape upon Sensing Guanine Nucleotides in a Disease Mutant of Elongation Factor-like 1 (EFL1) GTPase

The final maturation step of the 60S ribosomal subunit requires the release of eukaryotic translation initiation factor 6 (human eIF6, yeast Tif6) to enter the pool of mature ribosomes capable of engaging in translation. This process is mediated by the concerted action of the Elongation Factor-like 1 (human EFL1, yeast Efl1) GTPase and its effector, the Shwachman-Bodian-Diamond syndrome protein (human SBDS, yeast Sdo1). Mutations in these proteins prevent the release of eIF6 and cause a disease known as Shwachman–Diamond Syndrome (SDS). While some mutations in EFL1 or SBDS result in insufficient proteins to meet the cell production of mature large ribosomal subunits, others do not affect the expression levels with unclear molecular defects. We studied the functional consequences of one such mutation using Saccharomyces cerevisiae Efl1 R1086Q, equivalent to human EFL1 R1095Q described in SDS patients. We characterised the enzyme kinetics and energetic basis outlining the recognition of this mutant to guanine nucleotides and Sdo1, and their interplay in solution. From our data, we propose a model where the conformational change in Efl1 depends on a long-distance network of interactions that are disrupted in mutant R1086Q, whereby Sdo1 and the guanine nucleotides no longer elicit the conformational changes previously described in the wild-type protein. These findings point to the molecular malfunction of an EFL1 mutant and its possible impact on SDS pathology.

Equivalence of the transition heat capacities of proteins and DNA

It has been reported for many globular proteins that the native heat capacity at 25 °C, per gram, is the same. This has been interpreted to indicate that heat capacity is a fundamental property of native proteins that provides important information on molecular structure and stability. Heat capacities for both proteins and DNA has been suggested to be related to universal effects of hydration/solvation on native structures. Here we report on results from thermal denaturation analysis of two well-known proteins, human serum albumin and lysozyme, and a short DNA hairpin. The transition heat capacities at the Tm for the three molecules were quantitatively evaluated by differential scanning calorimetry. When normalized per gram rather than per mol the transition heat capacities were found to be precisely equivalent. This observation for the transition heat capacities of the proteins is consistent with previous reports. However, an identical transition heat capacity for DNA has not been reported and was unexpected. Further analysis of the collected data suggested a mass dependence of hydration effects on thermal denaturation that is preserved at the individual protein amino acid and DNA base levels. Equivalence of transition heat capacities suggests the possibility of a universal role of hydration effects on the thermal stability of both proteins and DNA.

Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy

SignificanceUnderstanding the molecular forces driving the unfolded polypeptide chain to self-assemble into a functional native structure remains an open question. However, identifying the states visited during protein folding (e.g., the transition state between the unfolded and native states) is tricky due to their transient nature. Here, we introduce calorimetric force spectroscopy in a temperature jump optical trap to determine the enthalpy, entropy, and heat capacity of the transition state of protein barnase. We find that the transition state has the properties of a dry molten globule, that is, high free energy and low configurational entropy, being structurally similar to the native state. This experimental single-molecule study characterizes the thermodynamic properties of the transition state in funneled energy landscapes.

Structural-Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble

The functioning of proteins is intimately tied to their fluctuations in the native ensemble. The structural-energetic features that determine fluctuation amplitudes and hence the shape of the underlying landscape, which in turn determine the magnitude of the functional output, are often confounded by multiple variables. Here, we employ the FF1 domain from human p190A RhoGAP protein as a model system to uncover the molecular basis for phosphorylation of a buried tyrosine, which is crucial to the transcriptional activity associated with transcription factor TFII-I. Combining spectroscopy, calorimetry, statistical-mechanical modeling, molecular simulations, and in vitro phosphorylation assays, we show that the FF1 domain samples a diverse array of conformations in its native ensemble, some of which are phosphorylation-competent. Upon eliminating unfavorable charge-charge interactions through a single charge-reversal (K53E) or charge-neutralizing (K53Q) mutation, we observe proportionately lower phosphorylation extents due to the altered structural coupling, damped equilibrium fluctuations, and a more compact native ensemble. We thus establish a conformational selection mechanism for phosphorylation in the FF1 domain with K53 acting as a "gatekeeper", modulating the solvent exposure of the buried tyrosine. Our work demonstrates the role of unfavorable charge-charge interactions in governing functional events through the modulation of native ensemble characteristics, a feature that could be prevalent in ordered protein domains.

How sticky are our proteins? Quantifying hydrophobicity of the human proteome

Summary

Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the solvent. These residues can play an important functional role, e.g. in protein-protein and membrane interactions. Here, we first investigate how hydrophobic protein surfaces are by providing three measures for surface hydrophobicity: the total hydrophobic surface area, the relative hydrophobic surface area and-using our MolPatch method-the largest hydrophobic patch. Secondly, we analyze how difficult it is to predict these measures from sequence: by adapting solvent accessibility predictions from NetSurfP2.0, we obtain well-performing prediction methods for the THSA and RHSA, while predicting LHP is more challenging. Finally, we analyze implications of exposed hydrophobic surfaces: we show that hydrophobic proteins typically have low expression, suggesting cells avoid an overabundance of sticky proteins.

Availability and implementation

The data underlying this article are available in GitHub at https://github.com/ibivu/hydrophobic_patches.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

Learning the Hydrophobic, Hydrophilic, and Aromatic Character of Amino Acids from Thermal Relaxation and Interfacial Thermal Conductance

In this study, the thermal relaxation of the 20 naturally occurring amino acids in water and in the protein lysozyme is investigated using transient nonequilibrium molecular dynamics simulations. By modeling the thermal relaxation process, the relaxation times of the amino acids in water occurs over a time scale covering 2-5 ps. For the hydrophobic amino acids, the relaxation time is controlled by the size of the hydrocarbon side chain, while for hydrophilic amino acids, the number of hydrogen bonds does not significantly affect the time scales of the heat dissipation. Our results show that the interfacial thermal conductance at the amino acid-water interface is in the range of 40-80 MW m^-2 K^-1. Hydrophobic and aromatic amino acids tend to have a lower interfacial thermal conductance. Notably, we show that amino acids can be correlated with their thermal relaxation times and molar masses, into simply connected phases with the same hydrophilicity, hydrophobicity, and aromaticity. The thermal relaxation slows down by a factor of up to five in the protein relative to that in water. In the case of the hydrophobic amino acids in the protein lysozyme, the slow down in the thermal relaxation relative to that in water appears to be controlled primarily by the size of the side chain.

Folding Free Energy Surfaces from Differential Scanning Calorimetry

Protein folding/unfolding processes involve a large number of weak, non-covalent interactions and are more appropriately described in terms of the movement of a point representing protein conformation in a plot of internal free energy versus conformational degrees of freedom. While these energy landscapes have an astronomically large number of dimensions, it has been shown that many relevant aspects of protein folding can be understood in terms of their projections onto a few relevant coordinates. Remarkably, such low-dimensional free energy surfaces can be obtained from experimental DSC data using suitable analytical models. Here, we describe the experimental procedures to be used to obtain the high-quality DSC data that are required for free-energy surface analysis.

Protective effects of combining monoclonal antibodies and vaccines against the Plasmodium falciparum circumsporozoite protein

Combinations of monoclonal antibodies (mAbs) against different epitopes on the same antigen synergistically neutralize many viruses. However, there are limited studies assessing whether combining human mAbs against distinct regions of the Plasmodium falciparum (Pf) circumsporozoite protein (CSP) enhances in vivo protection against malaria compared to each mAb alone or whether passive transfer of PfCSP mAbs would improve protection following vaccination against PfCSP. Here, we isolated a panel of human mAbs against the subdominant C-terminal domain of PfCSP (C-CSP) from a volunteer immunized with radiation-attenuated Pf sporozoites. These C-CSP-specific mAbs had limited binding to sporozoites in vitro that was increased by combination with neutralizing human "repeat" mAbs against the NPDP/NVDP/NANP tetrapeptides in the central repeat region of PfCSP. Nevertheless, passive transfer of repeat- and C-CSP-specific mAb combinations did not provide enhanced protection against in vivo sporozoite challenge compared to repeat mAbs alone. Furthermore, combining potent repeat-specific mAbs (CIS43, L9, and 317) that respectively target the three tetrapeptides (NPDP/NVDP/NANP) did not provide additional protection against in vivo sporozoite challenge. However, administration of either CIS43, L9, or 317 (but not C-CSP-specific mAbs) to mice that had been immunized with R21, a PfCSP-based virus-like particle vaccine that induces polyclonal antibodies against the repeat region and C-CSP, provided enhanced protection against sporozoite challenge when compared to vaccine or mAbs alone. Collectively, this study shows that while combining mAbs against the repeat and C-terminal regions of PfCSP provide no additional protection in vivo, repeat mAbs do provide increased protection when combined with vaccine-induced polyclonal antibodies. These data should inform the implementation of PfCSP human mAbs alone or following vaccination to prevent malaria infection.

Continuous Injection Isothermal Titration Calorimetry for In Situ Evaluation of Thermodynamic Binding Properties of Ligand-Receptor Binding Models

We utilize a continuous injection approach (CIA) rather than the traditional incremental injection approach (IIA) to deliver ligand (or receptor) to the calorimeter cell to evaluate thermodynamic binding parameters for three common ligand-receptor binding models-single independent, competitive, and two independent binding sites-using isothermal titration calorimetry (ITC). A general mathematical expression for the binding isotherm for any binding stoichiometry under continuous delivery of ligand (or receptor) resulting in an analytical solution for the thermodynamic binding parameters is presented. The advantages of CIA include reduction in experimental time, estimation of thermodynamic binding parameter values, and automation of the experiment since thermodynamic parameters are estimated in situ. We demonstrate the inherent advantages of CIA over IIA for the three binding models. For the single independent site model, we utilized the binding of Ba²⁺ ions to ethylenediaminetetraacetic acid (EDTA), while competitive binding was captured by titration of Ca²⁺ ions into a buffered solution of Ba²⁺ and EDTA. We experimentally simulated a two independent binding site system by injecting Ca²⁺ into a solution of EDTA and 1,3-diaminopropane-N,N,N',N'-tetraacetic acid (DPTA). The results demonstrate estimation of thermodynamic parameters with greater confidence and simultaneous reduction in the experimental time of 83% and titrating reagent of 50%, as compared to IIA.

FoldAffinity: binding affinities from nDSF experiments

Differential scanning fluorimetry (DSF) using the inherent fluorescence of proteins (nDSF) is a popular technique to evaluate thermal protein stability in different conditions (e.g. buffer, pH). In many cases, ligand binding increases thermal stability of a protein and often this can be detected as a clear shift in nDSF experiments. Here, we evaluate binding affinity quantification based on thermal shifts. We present four protein systems with different binding affinity ligands, ranging from nM to high μM. Our study suggests that binding affinities determined by isothermal analysis are in better agreement with those from established biophysical techniques (ITC and MST) compared to apparent K_ds obtained from melting temperatures. In addition, we describe a method to optionally fit the heat capacity change upon unfolding (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Delta {C}_{p}$$\end{document}ΔCp) during the isothermal analysis. This publication includes the release of a web server for easy and accessible application of isothermal analysis to nDSF data.

Investigation of the LCST-Thermoresponsive Behavior of Novel Oligo(Ethylene Glycol)-Modified Pentafluorostyrene Homopolymers

Amphiphilic tetrafluorostyrene monomers (EFS8) carrying in the para position an oligoethylene glycol chain containing 8 oxyethylenic units on average were synthesized and used for preparation via activator regenerated by electron transfer atom transfer radical polymerization (ARGET-ATRP) of the corresponding amphiphilic homopolymers (pEFS8-x) with different degrees of polymerization (x = 26 and 46). Combining light transmittance and nano-differential scanning calorimetry (n-DSC) measurements revealed that pEFS8-x homopolymers displayed a lower critical solution temperature (LCST) thermoresponsive behavior in water solutions. Moreover, n-DSC measurements revealed the presence in heating scans of a broad endothermic peak ascribable to the dehydration process of the polymer single chains (unimers) and their collapse into aggregates. Consistently, dynamic light scattering (DLS) measurements showed below the LCST the presence of small nanostructures with a hydrodynamic diameter size Dh of 6–7 nm, which collapsed into concentration-dependent larger multichain aggregates (Dh = 300–3000 nm) above LCST. Interestingly, n-DSC data showed that the unimer-aggregate transition was reversible up to a specific temperature (Trev) of each homopolymer, which in any case was higher than Tmax. When heating above Trev the transition was no longer reversible, causing the shift of Tonset and Tmax at lower values, thus suggesting an increase in hydrophobicity of the polymer systems associated with a temperature-dependent dehydration process.

Probing coupled conformational transitions of intrinsically disordered proteins in their interactions with target proteins

Intrinsically disordered proteins or regions (IDPs or IDRs) are abundant in the eukaryotic proteome and critical in regulation of dynamic cellular processes. Intensive structural investigations have proposed the molecular mechanisms of the interaction between IDRs and their binding partners. Here we extract the distinct thermodynamic features of coupled conformational transitions of IDRs founding the interaction mechanisms. We also present simulation tools to facilitate a design of the calorimetric experiments probing and quantifying the conformational transitions of IDRs. The suggested thermodynamic approach will further advance our understanding of distribution among multiple states of IDRs in their interactions with target molecules.

Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins

The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained.

Label-free imaging of fibroblast membrane interfaces and protein signatures with vibrational infrared photothermal and phase signals

Label-free vibrational imaging of biological samples has attracted significant interest due to its integration of structural and chemical information. Vibrational infrared photothermal amplitude and phase signal (VIPPS) imaging provide label-free chemical identification by targeting the characteristic resonances of biological compounds that are present in the mid-infrared fingerprint region (3 µm - 12 µm). High contrast imaging of subcellular features and chemical identification of protein secondary structures in unlabeled and labeled fibroblast cells embedded in a collagen-rich extracellular matrix is demonstrated by combining contrast from absorption signatures (amplitude signals) with sensitive detection of different heat properties (lock-in phase signals). We present that the detectability of nano-sized cell membranes is enhanced to well below the optical diffraction limit since the membranes are found to act as thermal barriers. VIPPS offers a novel combination of chemical imaging and thermal diffusion characterization that paves the way towards label-free imaging of cell models and tissues as well as the study of intracellular heat dynamics.

Origin of heat capacity increment in DNA folding: The hydration effect

BACKGROUND

Understanding DNA folding thermodynamics is crucial for prediction of DNA thermal stability. It is now well established that DNA folding is accompanied by a decrease of the heat capacity ∆c_{p, F}, however its molecular origin is not understood. In analogy to protein folding it has been assumed that this is due to dehydration of DNA constituents, however no evidence exists to support this conclusion.

METHODS

Here we analyze partial molar heat capacity of nucleic bases and nucleosides in aqueous solutions obtained from calorimetric experiments and calculate the hydration heat capacity contribution ∆c_p^hyd.

RESULTS

We present hydration heat capacity contributions of DNA constituents and show that they correlate with the solvent accessible surface area. The average contribution for nucleic base dehydration is +0.56 J mol^-1 K^-1 Å^-2 and can be used to estimate the ∆c_{p, F} contribution for DNA folding.

CONCLUSIONS

We show that dehydration is one of the major sources contributing to the observed ∆c_{p, F} increment in DNA folding. Other possible sources contributing to the overall ∆c_{p, F} should be significant but appear to compensate each other to high degree. The calculated ∆c_p^hyd for duplexes and noncanonical DNA structures agree excellently with the overall experimental ∆c_{p, F} values. By contrast, empirical parametrizations developed for proteins result in poor ∆c_p^hyd predictions and should not be applied to DNA folding.

GENERAL SIGNIFICANCE

Heat capacity is one of the main thermodynamic quantities that strongly affects thermal stability of macromolecules. At the molecular level the heat capacity in DNA folding stems from removal of water from nucleobases.

Thermodynamic Basis for Conformational Coupling in an ATP-Binding Cassette Exporter

ATP-binding cassette (ABC) transporters constitute one of the largest protein superfamilies, and they mediate the transport of diverse substrates across the membrane. The molecular mechanism for transducing the energy from ATP binding and hydrolysis into the conformational changes remains elusive. Here, we determined the thermodynamics underlying the ATP-induced global conformational switching for the ABC exporter TmrAB using temperature-resolved pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy. We show that a strong entropy-enthalpy compensation mechanism enables the closure of the nucleotide-binding domains (NBDs) over a wide temperature range. This is mechanically coupled with an outward opening of the transmembrane domains (TMDs) accompanied by an entropy gain. The conserved catalytic glutamate plays a key role in the overall energetics. Our results reveal the thermodynamic basis for the chemomechanical energy coupling in an ABC exporter and present a new strategy to explore the energetics of similar membrane protein complexes.

Binding Thermodynamics to Intrinsically Disordered Protein Domains

Many proteins are intrinsically disordered or contain one or more disordered domains. These domains can participate in binding interactions with other proteins or small ligands. Binding to intrinsically disordered protein domains requires the folding or structuring of those regions such that they can establish well-defined stoichiometric interactions. Since, in such a situation binding is coupled to folding, the energetics of those two events is reflected in the measured binding thermodynamics. In this protocol, we illustrate the thermodynamic differences between binding coupled to folding and binding independent of folding for the same protein. As an example, we use the HIV-1 envelope glycoprotein gp120 that contains structured as well as disordered domains. In the experiments presented, the binding of gp120 to molecules that bind to disordered regions and trigger structuring (CD4 or MAb 17b) and to molecules that bind to structured regions and do not induce conformational structuring (MAb b12) is discussed.

Rapid, Noninvasive, and Nondestructive Method for Biofilm Imaging on Metallic Surfaces Using Active Thermography

A simple, rapid, low-cost method was proposed for the imaging of Pseudomonas aeruginosa biofilms on metallic surfaces using an infrared camera. Stainless steel coupons were cooled to generate a thermal gradient in relation to biofilm for active thermography (AT). Both cooling and image acquisition times were optimized and the images obtained with AT were compared with those from scanning electron microscopy. A free software (Thermofilm) was developed for image processing and the results were compared with the software ImageJ, with good agreement (from 87.7 to 103.8%). Images of coupons treated with sanitizer (peracetic acid) were obtained to show the applicability of the proposed method for biofilm studies. All analytical steps could be performed in 3 min in a noncontact, nondestructive, low-cost, portable, and easy-to-use way.

How does cholinium cation surpass tetraethylammonium cation in amino acid-based ionic liquids for thermal and structural stability of serum albumins?

In this study, we report how similarly two serum albumins (bovine serum albumin (BSA) and human serum albumin (HSA)) respond in the presence of different concentration of aromatic amino acid based ionic liquids (AAILs), which are cholinium tryptophan [CHO][Trp]IL and tetraethylammonium tryptophan [TEA][Trp]IL. Extended results of thermodynamic stability indicate the extent to which both serum albumins differ in their thermal stability despite having structural similarity in presence of AAILs. To efficiently quantify the results, biomolecular interactions studies were carried out between serum albumins and AAILs with the help of differential scanning calorimetry (DSC), dynamic light scattering (DLS) and various spectroscopic techniques. DSC results illustrated that both AAILs are increasing the thermal stability of BSA and HSA, as per transition temperature (T_m) values, BSA (65.51 to 72.46 °C) and HSA (65.46 to 75.97 °C) have more thermal stability in the presence of [CHO][Trp]IL as compare to [TEA][Trp]IL, BSA (65.51 to 69.75 °C) and HSA (65.46 to 72.08 °C). Secondary structure results obtained using Dichroweb software and selcon calculations. Furthermore, to illustrate the specific binding of AAIL's cations or anions with the binding sites of BSA and HSA, the molecular docking studies were also performed using Molegro trail version v 6.0.

Human importin α3 and its N-terminal truncated form, without the importin-β-binding domain, are oligomeric species with a low conformational stability in solution

BACKGROUND

Eukaryotic cells have a continuous transit of macromolecules between the cytoplasm and the nucleus. Several carrier proteins are involved in this transport. One of them is importin α, which must form a complex with importin β to accomplish its function, by domain-swapping its 60-residue-long N terminus. There are several human isoforms of importin α; among them, importin α3 has a particularly high flexibility.

METHODS

We studied the conformational stability of intact importin α3 (Impα3) and its truncated form, where the 64-residue-long, N-terminal importin-β-binding domain (IBB) has been removed (ΔImpα3), in a wide pH range, with several spectroscopic, biophysical, biochemical methods and with molecular dynamics (MD).

RESULTS

Both species acquired native-like structure between pH 7 and 10.0, where Impα3 was a dimer (with an apparent self-association constant of ~10 μM) and ΔImpα3 had a higher tendency to self-associate than the intact species. The acquisition of secondary, tertiary and quaternary structure, and the burial of hydrophobic patches, occurred concomitantly. Both proteins unfolded irreversibly at physiological pH, by using either temperature or chemical denaturants, through several partially folded intermediates. The MD simulations support the presence of these intermediates.

CONCLUSIONS

The thermal stability of Impα3 at physiological pH was very low, but was higher than that of ΔImpα3. Both proteins were stable in a narrow pH range, and they unfolded at physiological pH populating several intermediate species.

GENERAL SIGNIFICANCE

The low conformational stability explains the flexibility of Impα3, which is needed to carry out its recognition of complex cargo sequences.

Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin in the multiphoton regime and biological relevance

How does chemistry scale in complexity to unerringly direct biological functions? Nass Kovacs et al. have shown that bacteriorhodopsin undergoes structural changes tantalizingly similar to the expected pathway even under excessive excitation. Is the protein structure so highly evolved that it directs all deposited energy into the designed function?

Impact of Heat on Coil Hydrodynamic Size Yields the Energetics of Denatured State Conformational Bias

Conformational equilibria in the protein denatured state have key roles regulating folding, stability, and function. The extent of conformational bias in the protein denatured state under folding conditions, however, has thus far proven elusive to quantify, particularly with regard to its sequence dependence and energetic character. To better understand the structural preferences of the denatured state, we analyzed both the sequence dependence to the mean hydrodynamic size of disordered proteins in water and the impact of heat on the coil dimensions, showing that the sequence dependence and thermodynamic energies associated with intrinsic biases for the α and polyproline II (PPII) backbone conformations can be obtained. Experiments that evaluate how the hydrodynamic size changes with compositional changes in the protein reveal amino acid specific preferences for PPII that are in good quantitative agreement with calorimetry-measured values from unfolded peptides and those inferred by survey of the protein coil library. At temperatures above 25 °C, the denatured state follows the predictions of a PPII-dominant ensemble. Heat effects on coil hydrodynamic size indicate the α bias is comparable to the PPII bias at cold temperatures. Though historically thought to give poor resolution to structural details, the hydrodynamic size of the unfolded state is found to be an effective reporter on the extent of the biases for the α and PPII backbone conformations.

Sequence Reversal Prevents Chain Collapse and Yields Heat-Sensitive Intrinsic Disorder

Sequence patterns of charge, hydrophobicity, hydrogen bonding, and other amino acid physicochemical properties contribute to mechanisms of protein folding, but how sequence composition and patterns influence the conformational dynamics of the denatured state ensemble is not fully understood. To investigate structure-sequence relationships in the denatured state, we reversed the sequence of staphylococcal nuclease and characterized its structure, thermodynamic character, and hydrodynamic radius using circular dichroism spectroscopy, dynamic light scattering, analytical ultracentrifugation, and size-exclusion chromatography as a function of temperature. The macromolecular size of "Retro-nuclease" is highly expanded in solution with characteristics similar to biological intrinsically disordered proteins. In contradistinction to a disordered state, Retro-nuclease exhibits a broad sigmoid transition of its hydrodynamic dimensions as temperature is increased, indicating a thermodynamically controlled compaction. Counterintuitively, the magnitude of these temperature-induced hydrodynamic changes exceed that observed from thermal denaturation of folded unaltered staphylococcal nuclease. Undetectable by calorimetry and intrinsic tryptophan fluorescence, the lack of heat capacity or fluorescence changes throughout the thermal transition indicate canonical hydrophobic collapse did not drive the Retro-nuclease structural transitions. Temperature-dependent circular dichroism spectroscopy performed on Retro-nuclease and computer simulations correlate to temperature sensitivity in the intrinsic sampling of backbone conformations for polyproline II and α-helix. The experimental results indicate a role for sequence direction in mediating the collapse of the polypeptide chain, whereas the simulation trends illustrate the generality of the observed heat effects on disordered protein structure.

Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA

The amplitude of thermodynamic fluctuations in biological macromolecules determines their conformational behavior, dimensions, nature of phase transitions and effectively their specificity and affinity, thus contributing to fine-tuned molecular recognition. Unique among large-scale conformational changes in proteins are temperature-induced collapse transitions in intrinsically disordered proteins (IDPs). Here, we show that CytR DNA-binding domain, an IDP that folds on binding DNA, undergoes a coil-to-globule transition with temperature in the absence of DNA while exhibiting energetically decoupled local and global structural rearrangements, and maximal thermodynamic fluctuations at the optimal bacterial growth temperature. The collapse is shown to be a continuous transition through a combination of statistical-mechanical modeling and all-atom implicit solvent simulations. Surprisingly, CytR binds single-site cognate DNA with negative cooperativity, described by Hill coefficients less than one, resulting in a graded binding response. We show that heterogeneity arising from varying binding-competent CytR conformations or orientations at the single-molecular level contributes to negative binding cooperativity at the level of bulk measurements due to the conflicting requirements of collapse transition, large fluctuations and folding-upon-binding. Our work reports strong evidence for functionally driven thermodynamic fluctuations in determining the extent of collapse and disorder with implications in protein search efficiency of target DNA sites and regulation.

Binding of ferredoxin NADP+ oxidoreductase (FNR) to plant photosystem I

The binding of FNR to PSI has been postulated long ago, however, a clear evidence is still missing. In this work, using isothermal titration calorimetry (ITC), we found that FNR binds to photosystem I with its light harvesting complex I (PSI-LHCI) from C. reinhardtii with a 1:1 stoichiometry, a Kd of ~0.8 μM and ∆H of -20.7 kcal/mol. Titrations at different temperatures were used to determine the heat capacity change, ∆CP, of the binding, through which the size of the interface area between the proteins was assessed as ~3000 Ų. In a different set of ITC experiments, introduction of various sucrose concentrations was used to estimate that ~95 water molecules are released to the solvent. These observations support the notion of a binding site shared by few of the photosystem I - light harvesting complex I (PSI-LHCI) subunits in addition to PsaE. Based on these results, a hypothetical model was built for the binding site of FNR at PSI, using known crystallographic structures of: cyanobacterial PSI in complex with ferredoxin (Fd), plant PSI-LHCI and Fd:FNR complex from cyanobacteria. FNR binding site location is proposed to be at the foot of the stromal ridge and above the inner LHCI belt. It is expected to form contacts with PsaE, PsaB, PsaF and at least one of the LHCI. In addition, a ~4.5-fold increased affinity between FNR and PSI-LHCI under crowded 1 M sucrose environment led us to conclude that in C. reinhardtii FNR also functions as a subunit of PSI-LHCI.

Structural and Thermodynamic Analysis of HIV-1 Fusion Inhibition Using Small gp41 Mimetic Proteins

Development of effective inhibitors of the fusion between HIV-1 and the host cell membrane mediated by gp41 continues to be a grand challenge due to an incomplete understanding of the molecular and mechanistic details of the fusion process. We previously developed single-chain, chimeric proteins (named covNHR) that accurately mimic the N-heptad repeat (NHR) region of gp41 in a highly stable coiled-coil conformation. These molecules bind strongly to peptides derived from the gp41 C-heptad repeat (CHR) and are potent and broad HIV-1 inhibitors. Here, we investigated two covNHR variants differing in two mutations, V10E and Q123R (equivalent to V38E and Q40R in gp41 sequence) that reproduce the effect of HIV-1 mutations associated with resistance to fusion inhibitors, such as T20 (enfuvirtide). A detailed calorimetric analysis of the binding between the covNHR proteins and CHR peptides (C34 and T20) reveals drastic changes in affinity due to the mutations as a result of local changes in interactions at the site of T20 resistance. The crystallographic structure of the covNHR:C34 complex shows a virtually identical CHR-NHR binding interface to that of the post-fusion structure of gp41 and underlines an important role of buried interfacial water molecules in binding affinity and in development of resistance against CHR peptides. Despite the great difference in affinity, both covNHR variants demonstrate strong inhibitory activity for a wide variety of HIV-1 strains. These properties support the high potential of these covNHR proteins as new potent HIV-1 inhibitors. Our results may guide future inhibition approaches.

Engineering Order and Cooperativity in a Disordered Protein

Structural disorder in proteins arises from a complex interplay between weak hydrophobicity and unfavorable electrostatic interactions. The extent to which the hydrophobic effect contributes to the unique and compact native state of proteins is, however, confounded by large compensation between multiple entropic and energetic terms. Here we show that protein structural order and cooperativity arise as emergent properties upon hydrophobic substitutions in a disordered system with non-intuitive effects on folding and function. Aided by sequence-structure analysis, equilibrium, and kinetic spectroscopic studies, we engineer two hydrophobic mutations in the disordered DNA-binding domain of CytR that act synergistically, but not in isolation, to promote structure, compactness, and stability. The double mutant, with properties of a fully ordered domain, exhibits weak cooperativity with a complex and rugged conformational landscape. The mutant, however, binds cognate DNA with an affinity only marginally higher than that of the wild type, though nontrivial differences are observed in the binding to noncognate DNA. Our work provides direct experimental evidence of the dominant role of non-additive hydrophobic effects in shaping the molecular evolution of order in disordered proteins and vice versa, which could be generalized to even folded proteins with implications for protein design and functional manipulation.

Echo dephasing and heat capacity from constrained and unconstrained dynamics of triiodothyronine nuclear receptor protein

The objective of this study is to observe the echo feature curves, vibrational dephasing, and heat capacity of a protein-hormone system taking thyroid hormone receptor-beta (THR-β) as an example. Constrained and unconstrained molecular dynamics simulations are performed by implementing the theory of velocity reassignments to probe the phase coherent state in terms of echo pulses. The constrained vibrations are incorporated by adjusting rigid bonds to all hydrogen atoms with an integrator parameter of 2 fs/step in order to reduce the degrees of freedom whereas 1 fs/step is used in the free vibrations of the atomic cluster. The nature of temperature auto-correlation functions changes so that echo feature curves also show a distinct nature in the cases of constrained and unconstrained vibrations. There is a large variation in kinetic temperature and internal potential energy in the echo time zone. The temperature rate of change of internal potential energy is the main contributor to the heat capacity of the native state protein-hormone system. The heat capacity of proteins estimated from this technique is in good agreement with the values from experiments. This study shows that triiodothyronine (T3) hormone makes some differences in heat capacity upon binding to the THR-β ligand binding domain (LBD). The physical properties of unliganded THR-β and T3-bound THR-β LBD in the cases of constrained and unconstrained dynamics are observed distinctly under the effect of anharmonicity on the phase coherent state of normal modes and the dephasing time lies in a range of 0.6-0.8 ps when the systems are perturbed suddenly.