Entropy in molecular recognition by proteins

Quantitative Prediction of Protein-Polyelectrolyte Binding Thermodynamics: Adsorption of Heparin-Analog Polysulfates to the SARS-CoV-2 Spike Protein RBD

Interactions of polyelectrolytes (PEs) with proteins play a crucial role in numerous biological processes, such as the internalization of virus particles into host cells. Although docking, machine learning methods, and molecular dynamics (MD) simulations are utilized to estimate binding poses and binding free energies of small-molecule drugs to proteins, quantitative prediction of the binding thermodynamics of PE-based drugs presents a significant obstacle in computer-aided drug design. This is due to the sluggish dynamics of PEs caused by their size and strong charge-charge correlations. In this paper, we introduce advanced sampling methods based on a force-spectroscopy setup and theoretical modeling to overcome this barrier. We exemplify our method with explicit solvent all-atom MD simulations of the interactions between anionic PEs that show antiviral properties, namely heparin and linear polyglycerol sulfate (LPGS), and the SARS-CoV-2 spike protein receptor binding domain (RBD). Our prediction for the binding free-energy of LPGS to the wild-type RBD matches experimentally measured dissociation constants within thermal energy, k B T, and correctly reproduces the experimental PE-length dependence. We find that LPGS binds to the Delta-variant RBD with an additional free-energy gain of 2.4 k B T, compared to the wild-type RBD, due to the additional presence of two mutated cationic residues contributing to the electrostatic energy gain. We show that the LPGS-RBD binding is solvent dominated and enthalpy driven, though with a large entropy-enthalpy compensation. Our method is applicable to general polymer adsorption phenomena and predicts precise binding free energies and reconfigurational friction as needed for drug and drug-delivery design.

Insights into Ligand-Mediated Activation of an Oligomeric Ring-Shaped Gene-Regulatory Protein from Solution- and Solid-State NMR

The 91 kDa oligomeric ring-shaped ligand binding protein TRAP (trp RNA binding attenuation protein) regulates the expression of a series of genes involved in tryptophan (Trp) biosynthesis in bacilli. When cellular Trp levels rise, the free amino acid binds to sites buried in the interfaces between each of the 11 (or 12, depending on the species) protomers in the ring. Crystal structures of Trp-bound TRAP show the Trp ligands are sequestered from solvent by a pair of loops from adjacent protomers that bury the bound ligand via polar contacts to several threonine residues. Binding of the Trp ligands occurs cooperatively, such that successive binding events occur with higher apparent affinity but the structural basis for this cooperativity is poorly understood. We used solution methyl-TROSY NMR relaxation experiments focused on threonine and isoleucine sidechains, as well as magic angle spinning solid-state NMR 13C-13C and 15N-13C chemical shift correlation spectra on uniformly labeled samples recorded at 800 and 1200 MHz, to characterize the structure and dynamics of the protein. Methyl 13C relaxation dispersion experiments on ligand-free apo TRAP revealed concerted exchange dynamics on the µs-ms time scale, consistent with transient sampling of conformations that could allow ligand binding. Cross-correlated relaxation experiments revealed widespread disorder on fast timescales. Chemical shifts for methyl-bearing side chains in apo- and Trp-bound TRAP revealed subtle changes in the distribution of sampled sidechain rotameric states. These observations reveal a pathway and mechanism for induced conformational changes to generate homotropic Trp-Trp binding cooperativity.

Accuracy and Reproducibility of Lipari-Szabo Order Parameters From Molecular Dynamics

The Lipari-Szabo generalized order parameter probes the picosecond to nanosecond time scale motions of a protein and is useful for rationalizing a multitude of biological processes such as protein recognition and ligand binding. Although these fast motions are an important and intrinsic property of proteins, it remains unclear what simulation conditions are most suitable to reproduce methyl symmetry axis side chain order parameter data (Saxis2) from molecular dynamics simulations. In this study, we show that, while Saxis2 tends to converge within tens of nanoseconds, it is essential to run 10 to 20 replicas starting from configurations close to the experimental structure to obtain the best agreement with experimental Saxis2 values. Additionally, in a comparison of force fields, AMBER ff14SB outperforms CHARMM36m in accurately capturing these fast time scale motions, and we suggest that the origin of this performance gap is likely attributed to differences in side chain torsional parametrization and not due to differences in the global protein conformations sampled by the force fields. This study provides insight into obtaining accurate and reproducible Saxis2 values from molecular simulations and underscores the necessity of using replica simulations to compute equilibrium properties.

Positive activation entropy of Bacillus circulans xylanase catalyzed ONPX2 hydrolysis: A mechanistic and engineering study

Transition state (TS) stabilization by enzymes greatly accelerates catalytic reactions. For some enzymes, the TS complex has entropy higher than enzyme substrate (ES) complex. But the origin of favorable entropy remains unclear. In this work, we studied the mechanism of Bacillus Circulans xylanase (BCX) 11 catalyzed o-nitrophenyl β-xylobioside (ONPX2) glycoside hydrolysis. The catalytic reaction exhibits a positive activation entropy, and an increase in ionic strength leads to a decrease in entropy without affecting the activation free energy, indicating that the entropy is predominantly influenced by electrostatic forces. Moreover, NMR measurements of electrostatic attractions within the active site demonstrate a positive entropy, aligning with molecular dynamics (MD) simulations showing that electrostatic interactions contribute to the entropic stabilization of the TS complex. These findings suggest that the positive entropy primarily originates from alterations in electrostatic interactions due to the formation of the oxocarbenium ion at C1 in the TS. Differences of electrostatic interactions in ES and TS modify hydrogen bonding of surrounding residues in the active site which causes their side chain dynamics and thus conformational entropy changes. Residues critical for the positive activation entropy are identified. A new BCX mutant with an increased activation entropy and catalytic activity is found.

Deuterium spin relaxation of fractionally deuterated ribonuclease H using paired 475 and 950 MHz NMR spectrometers

Deuterium (2H) spin relaxation of 13CH2D methyl groups has been widely applied to investigate picosecond-to-nanosecond conformational dynamics in proteins by solution-state NMR spectroscopy. The B0 dependence of the 2H spin relaxation rates is represented by a linear relationship between the spectral density function at three discrete frequencies J(0), J(ωD) and J(2ωD). In this study, the linear relation between 2H relaxation rates at B0 fields separated by a factor of two and the interpolation of rates at intermediate frequencies are combined for a more robust approach for spectral density mapping. The general usefulness of the approach is demonstrated on a fractionally deuterated (55%) and alternate 13C-12C labeled sample of E. coli RNase H. Deuterium relaxation rate constants (R1, R1ρ, RQ, RAP) were measured for 57 well-resolved 13CH2D moieties in RNase H at 1H frequencies of 475 MHz, 500 MHz, 900 MHz, and 950 MHz. The spectral density mapping of the 475/950 MHz data combination was performed independently and jointly to validate the expected relationship between data recorded at B0 fields separated by a factor of two. The final analysis was performed by jointly analyzing 475/950 MHz rates with 700 MHz rates interpolated from 500/900 MHz data to yield six J(ωD) values for each methyl peak. The J(ω) profile for each peak was fit to the original (τM, Sf2, τf) or extended model-free function (τM, Sf2, Ss2, τf, τs) to obtain optimized dynamic parameters.

Quantification of thermodynamic effects of carbohydrate multivalency on avidity using synthetic discrete glycooligomers

A quantitative understanding of thermodynamic effects of avidity in biomolecular interactions is important. Herein, we synthesized discrete glycooligomers and evaluated their interactions with a model protein using isothermal titration calorimetry. The dimeric glycooligomer exhibited higher binding constants compared to the glycomonomer, attributed to the reduced conformational entropy loss through local presentation of multiple carbohydrate units. Conversely, divalent glycoligands with polyethylene glycol linkers, aiming for multivalent binding, showed enhanced interactions through increased enthalpy. These findings emphasize the importance of distinguishing between the "local avidity" and the "multipoint avidity".

Structural Adaptation of Secondary p53 Binding Sites on MDM2 and MDMX

The thermodynamics of secondary p53 binding sites on MDM2 and MDMX were evaluated using p53 peptides containing residues 16-29, 17-35, and 1-73. All the peptides had large, negative heat capacity (ΔCp), consistent with the burial of p53 residues F19, W23, and L26 in the primary binding sites of MDM2 and MDMX. MDMX has a higher affinity and more negative ΔCp than MDM2 for p5317-35, which is due to MDMX stabilization and not additional interactions with the secondary binding site. ΔCp measurements show binding to the secondary site is inhibited by the disordered tails of MDM2 for WT p53 but not a more helical mutant where proline 27 is changed to alanine. This result is supported by all-atom molecular dynamics simulations showing that p53 residues 30-35 turn away from the disordered tails of MDM2 in P27A17-35 and make direct contact with this region in p5317-35. Molecular dynamics simulations also suggest that an intramolecular methionine-aromatic motif found in both MDM2 and MDMX structurally adapts to support multiple p53 binding modes with the secondary site. ΔCp measurements also show that tighter binding of the P27A mutant to MDM2 and MDMX is due to increased helicity, which reduces the energetic penalty associated with coupled folding and binding. Our results will facilitate the design of selective p53 inhibitors for MDM2 and MDMX.

Computer-aided molecular design and optimization of potent inhibitors disrupting APC‒Asef interaction

Colorectal cancer (CRC) is the second leading cause of cancer mortality worldwide. At initial diagnosis, approximately 20% of patients are diagnosed with metastatic CRC (mCRC). Although the APC‒Asef interaction is a well-established target for mCRC therapy, the discovery and development of effective and safe drugs for mCRC patients remains an urgent and challenging endeavor. In this study, we identified a novel structural scaffold based on MAI inhibitors, the first-in-class APC‒Asef inhibitors we reported previously. ONIOM model-driven optimizations of the N-terminal cap and experimental evaluations of inhibitory activity were performed, and 24-fold greater potency was obtained with the best inhibitor compared to the parental compound. In addition, the cocrystal structure validated that the two-layer π‒π stacking interactions were essential for inhibitor stabilization in the bound state. Furthermore, in vitro and in vivo studies have demonstrated that novel inhibitors suppressed lung metastasis in CRC by disrupting the APC‒Asef interaction. These results provide an intrinsic structural basis to further explore drug-like molecules for APC‒Asef-mediated CRC therapy.

Insights into Ligand-Mediated Activation of an Oligomeric Ring-Shaped Gene-Regulatory Protein from Solution- and Solid-State NMR

The 91 kDa oligomeric ring-shaped ligand binding protein TRAP (trp RNA binding attenuation protein) regulates the expression of a series of genes involved in tryptophan (Trp) biosynthesis in bacilli. When cellular Trp levels rise, the free amino acid binds to sites buried in the interfaces between each of the 11 (or 12, depending on the species) protomers in the ring. Crystal structures of Trp-bound TRAP show the Trp ligands are sequestered from solvent by a pair of loops from adjacent protomers that bury the bound ligand via polar contacts to several threonine residues. Binding of the Trp ligands occurs cooperatively, such that successive binding events occur with higher apparent affinity but the structural basis for this cooperativity is poorly understood. We used solution methyl-TROSY NMR relaxation experiments focused on threonine and isoleucine sidechains, as well as magic angle spinning solid-state NMR 13C-13C and 15N-13C chemical shift correlation spectra on uniformly labeled samples recorded at 800 and 1200 MHz, to characterize the structure and dynamics of the protein. Methyl 13C relaxation dispersion experiments on ligand-free apo TRAP revealed concerted exchange dynamics on the μs-ms time scale, consistent with transient sampling of conformations that could allow ligand binding. Cross-correlated relaxation experiments revealed widespread disorder on fast timescales. Chemical shifts for methyl-bearing side chains in apo- and Trp-bound TRAP revealed subtle changes in the distribution of sampled sidechain rotameric states. These observations reveal a pathway and mechanism for induced conformational changes to generate homotropic Trp-Trp binding cooperativity.

Sorting drug conformers in enzyme active sites: the XTB way

In the present study, we have used the MEI196 set of interaction energies to investigate low-cost computational chemistry approaches for the calculation of binding between a molecule and its environment. Density functional theory (DFT) methods, when used with the vDZP basis set, yield good agreement with the reference energies. On the other hand, semi-empirical methods are less accurate as expected. By examining different groups of systems within MEI196 that contain species of a similar nature, we find that chemical similarity leads to cancellation of errors in the calculation of relative binding energies. Importantly, the semi-empirical method GFN1-xTB (XTB1) yields reasonable results for this purpose. We have thus further assessed the performance of XTB1 for calculating relative energies of docking poses of substrates in enzyme active sites represented by cluster models or within the ONIOM protocol. The results support the observations on error cancellation. This paves the way for the use of XTB1 in parts of large-scale virtual screening workflows to accelerate the drug discovery process.

Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments

Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.

Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions

Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298 K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.

Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes

The functions of many proteins are associated with interconversions among conformational substates. However, these substates can be difficult to measure experimentally, and determining contributions from hydration changes can be especially difficult. Here, we assessed the use of pressure perturbations to sample the substates accessible to the Escherichia coli lactose repressor protein (LacI) in various liganded forms. In the presence of DNA, the regulatory domain of LacI adopts an Open conformation that, in the absence of DNA, changes to a Closed conformation. Increasing the simulation pressure prevented the transition from an Open to a Closed conformation, in a similar manner to the binding of DNA and anti-inducer, ONPF. The results suggest the hydration of specific residues play a significant role in determining the population of different LacI substates and that simulating pressure perturbation could be useful for assessing the role of hydration changes that accompany functionally-relevant amino acid substitutions.

Isothermal Titration Calorimetry to Study Plant Peptide Ligand-Receptor Interactions

The field of plant receptor biology has rapidly expanded in the past three decades. However, the demonstration of direct interaction between receptor-ligand pairs remains a challenge. Identifying and quantifying protein-ligand interactions is crucial for understanding how they regulate certain physiological processes. An important aspect is the quantification of different parameters of the interaction, like binding affinity, kinetics, and ligand specificity that drive the formation of signaling complexes. In this chapter, we discuss Isothermal Titration Calorimetry (ITC) as a label-free technique to measure thermodynamic parameters of ligand binding with high accuracy and reproducibility. We provide a detailed guideline how to design, perform, analyze, and interpret ITC measurements using as an example the interaction between the SCHENGEN3/GASSHO1 (SGN3/GSO1) leucine-rich repeat receptor-like kinase and its sulfated peptide ligand CASPARIAN STRIP INTEGRITY FACTOR 2 (CIF2).

Conformational entropy in molecular recognition of intrinsically disordered proteins

Broad conformational ensembles make intrinsically disordered proteins or regions entropically intriguing. Although methodologically challenging and understudied, emerging studies into their changes in conformational entropy (ΔS°conf) upon complex formation have provided both quantitative and qualitative insight. Recent work based on thermodynamics from isothermal titration calorimetry and NMR spectroscopy uncovers an expanded repertoire of regulatory mechanisms, where ΔS°conf plays roles in partner selection, state behavior, functional buffering, allosteric regulation, and drug design. We highlight these mechanisms to display the large entropic reservoir of IDPs for the regulation of molecular communication. We call upon the field to make efforts to contribute to this insight as more studies are needed for forwarding mechanistic decoding of intrinsically disordered proteins and their complexes.

Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics

All protein simulations are conducted with varying degrees of simplification, oftentimes with unknown ramifications about how these simplifications affect the interpretability of the results. In this work, we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: (1) glycosylated neuraminidase in a whole virion (i.e., crowded membrane) environment, (2) glycosylated neuraminidase in its own lipid bilayer, and (3) unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting the solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large-scale conformational change, while making the protein structure more compact. Understanding these effects informs what factors one must consider in attempting to recapture the desired level of physical accuracy.

Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions

Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.

Driving forces of the complex formation between highly charged disordered proteins

Highly disordered complexes between oppositely charged intrinsically disordered proteins present a new paradigm of biomolecular interactions. Here, we investigate the driving forces of such interactions for the example of the highly positively charged linker histone H1 and its highly negatively charged chaperone, prothymosin α (ProTα). Temperature-dependent single-molecule Förster resonance energy transfer (FRET) experiments and isothermal titration calorimetry reveal ProTα-H1 binding to be enthalpically unfavorable, and salt-dependent affinity measurements suggest counterion release entropy to be an important thermodynamic driving force. Using single-molecule FRET, we also identify ternary complexes between ProTα and H1 in addition to the heterodimer at equilibrium and show how they contribute to the thermodynamics observed in ensemble experiments. Finally, we explain the observed thermodynamics quantitatively with a mean-field polyelectrolyte theory that treats counterion release explicitly. ProTα-H1 complex formation resembles the interactions between synthetic polyelectrolytes, and the underlying principles are likely to be of broad relevance for interactions between charged biomolecules in general.

Temperature as a modulator of allosteric motions and crosstalk in mesophilic and thermophilic enzymes

Mesophilic and thermophilic enzyme counterparts are often studied to understand how proteins function under harsh conditions. To function well outside of standard temperature ranges, thermophiles often tightly regulate their structural ensemble through intra-protein communication (via allostery) and altered interactions with ligands. It has also become apparent in recent years that the enhancement or diminution of allosteric crosstalk can be temperature-dependent and distinguish thermophilic enzymes from their mesophilic paralogs. Since most studies of allostery utilize chemical modifications from pH, mutations, or ligands, the impact of temperature on allosteric function is comparatively understudied. Here, we discuss the biophysical methods, as well as critical case studies, that dissect temperature-dependent function of mesophilic-thermophilic enzyme pairs and their allosteric regulation across a range of temperatures.

Mixed, nonclassical behavior in a classic allosteric protein

Allostery is a major driver of biological processes requiring coordination. Thus, it is one of the most fundamental and remarkable phenomena in nature, and there is motivation to understand and manipulate it to a multitude of ends. Today, it is often described in terms of two phenomenological models proposed more than a half-century ago involving only T(tense) or R(relaxed) conformations. Here, methyl-based NMR provides extensive detail on a dynamic T to R switch in the classical dimeric allosteric protein, yeast chorismate mutase (CM), that occurs in the absence of substrate, but only with the activator bound. Switching of individual subunits is uncoupled based on direct observation of mixed TR states in the dimer. This unique finding excludes both classic models and solves the paradox of a coexisting hyperbolic binding curve and highly skewed substrate-free T-R equilibrium. Surprisingly, structures of the activator-bound and effector-free forms of CM appear the same by NMR, providing another example of the need to account for dynamic ensembles. The apo enzyme, which has a sigmoidal activity profile, is shown to switch, not to R, but to a related high-energy state. Thus, the conformational repertoire of CM does not just change as a matter of degree depending on the allosteric input, be it effector and/or substrate. Rather, the allosteric model appears to completely change in different contexts, which is only consistent with modern ensemble-based frameworks.

Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics

All protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy.

Engineering the Active Site Lid Dynamics to Improve the Catalytic Efficiency of Yeast Cytosine Deaminase

Conformational dynamics is important for enzyme catalysis. However, engineering dynamics to achieve a higher catalytic efficiency is still challenging. In this work, we develop a new strategy to improve the activity of yeast cytosine deaminase (yCD) by engineering its conformational dynamics. Specifically, we increase the dynamics of the yCD C-terminal helix, an active site lid that controls the product release. The C-terminal is extended by a dynamical single α-helix (SAH), which improves the product release rate by up to ~8-fold, and the overall catalytic rate kcat by up to ~2-fold. It is also shown that the kcat increase is due to the favorable activation entropy change. The NMR H/D exchange data indicate that the conformational dynamics of the transition state analog complex increases as the helix is extended, elucidating the origin of the enhanced catalytic entropy. This study highlights a novel dynamics engineering strategy that can accelerate the overall catalysis through the entropy-driven mechanism.

Deep mining of the protein energy landscape

For over half a century, it has been known that protein molecules naturally undergo extensive structural fluctuations, and that these internal motions are intimately related to their functional properties. The energy landscape view has provided a powerful framework for describing the various physical states that proteins visit during their lifetimes. This Perspective focuses on the commonly neglected and often disparaged axis of the protein energy landscape: entropy. Initially seen largely as a barrier to functionally relevant states of protein molecules, it has recently become clear that proteins retain considerable conformational entropy in the "native" state, and that this entropy can and often does contribute significantly to the free energy of fundamental protein properties, processes, and functions. NMR spectroscopy, molecular dynamics simulations, and emerging crystallographic views have matured in parallel to illuminate dynamic disorder of the "ground state" of proteins and their importance in not only transiting between biologically interesting structures but also greatly influencing their stability, cooperativity, and contribution to critical properties such as allostery.

Ligands selectively tune the local and global motions of neurotensin receptor 1 (NTS1)

Nuclear magnetic resonance (NMR) studies have revealed that fast methyl sidechain dynamics can report on entropically-driven allostery. Yet, NMR applications have been largely limited to the super-microsecond motional regimes of G protein-coupled receptors (GPCRs). We use ¹³C^ε-methionine chemical shift-based global order parameters to test if ligands affect the fast dynamics of a thermostabilized GPCR, neurotensin receptor 1 (NTS₁). We establish that the NTS₁ solution ensemble includes substates with lifetimes on several, discrete timescales. The longest-lived states reflect those captured in agonist- and inverse agonist-bound crystal structures, separated by large energy barriers. We observe that the rapid fluctuations of individual methionine residues, superimposed on these long-lived states, respond collectively with the degree of fast, global dynamics correlating with ligand pharmacology. This approach lends confidence to interpreting spectra in terms of local structure and methyl dihedral angle geometry. The results suggest a role for sub-microsecond dynamics and conformational entropy in GPCR ligand discrimination.

Thermodynamic analysis of an entropically driven, high-affinity nanobody-HIV p24 interaction

Protein-protein interactions are fundamental to life processes. Complementary computational, structural, and biophysical studies of these interactions enable the forces behind their specificity and strength to be understood. Antibody fragments such as single-chain antibodies have the specificity and affinity of full antibodies but a fraction of their size, expediting whole molecule studies and distal effects without exceeding the computational capacity of modeling systems. We previously reported the crystal structure of a high-affinity nanobody 59H10 bound to HIV-1 capsid protein p24 and deduced key interactions using all-atom molecular dynamics simulations. We studied the properties of closely related medium (37E7) and low (48G11) affinity nanobodies, to understand how changes of three (37E7) or one (48G11) amino acids impacted these interactions; however, the contributions of enthalpy and entropy were not quantified. Here, we report the use of qualitative and quantitative experimental and in silico approaches to separate the contributions of enthalpy and entropy. We used complementary circular dichroism spectroscopy and molecular dynamics simulations to qualitatively delineate changes between nanobodies in isolation and complexed with p24. Using quantitative techniques such as isothermal titration calorimetry alongside WaterMap and Free Energy Perturbation protocols, we found the difference between high (59H10) and medium (37E7) affinity nanobodies on binding to HIV-1 p24 is entropically driven, accounted for by the release of unstable waters from the hydrophobic surface of 59H10. Our results provide an exemplar of the utility of parallel in vitro and in silico studies and highlight that differences in entropic interactions between amino acids and water molecules are sufficient to drive orders of magnitude differences in affinity.

Locating dynamic contributions to allostery via determining rates of vibrational energy transfer

Determining rates of energy transfer across non-covalent contacts for different states of a protein can provide information about dynamic and associated entropy changes during transitions between states. We investigate the relationship between rates of energy transfer across polar and nonpolar contacts and contact dynamics for the β₂-adrenergic receptor, a rhodopsin-like G-protein coupled receptor, in an antagonist-bound inactive state and agonist-bound active state. From structures sampled during molecular dynamics (MD) simulations, we find the active state to have, on average, a lower packing density, corresponding to generally more flexibility and greater entropy than the inactive state. Energy exchange networks (EENs) are computed for the inactive and active states from the results of the MD simulations. From the EENs, changes in the rates of energy transfer across polar and nonpolar contacts are found for contacts that remain largely intact during activation. Change in dynamics of the contact, and entropy associated with the dynamics, can be estimated from the change in rates of energy transfer across the contacts. Measurement of change in the rates of energy transfer before and after the transition between states thereby provides information about dynamic contributions to activation and allostery.

Pressure, motion, and conformational entropy in molecular recognition by proteins

The thermodynamics of molecular recognition by proteins is a central determinant of complex biochemistry. For over a half-century, detailed cryogenic structures have provided deep insight into the energetic contributions to ligand binding by proteins. More recently, a dynamical proxy based on NMR-relaxation methods has revealed an unexpected richness in the contributions of conformational entropy to the thermodynamics of ligand binding. Here, we report the pressure dependence of fast internal motion within the ribonuclease barnase and its complex with the protein barstar. In what we believe is a first example, we find that protein dynamics are conserved along the pressure-binding thermodynamic cycle. The femtomolar affinity of the barnase-barstar complex exists despite a penalty by -TΔS_conf of +11.7 kJ/mol at ambient pressure. At high pressure, however, the overall change in side-chain dynamics is zero, and binding occurs with no conformational entropy penalty, suggesting an important role of conformational dynamics in the adaptation of protein function to extreme environments. Distinctive clustering of the pressure sensitivity is observed in response to both pressure and binding, indicating the presence of conformational heterogeneity involving less efficiently packed alternative conformation(s). The structural segregation of dynamics observed in barnase is striking and shows how changes in both the magnitude and the sign of regional contributions of conformational entropy to the thermodynamics of protein function are possible.

Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery

EF-hand Ca2+-binding proteins (CBPs), such as S100 proteins (S100s) and calmodulin (CaM), are signaling proteins that undergo conformational changes upon increasing intracellular Ca2+. Upon binding Ca2+, S100 proteins and CaM interact with protein targets and induce important biological responses. The Ca2+-binding affinity of CaM and most S100s in the absence of target is weak (CaKD > 1 μM). However, upon effector protein binding, the Ca2+ affinity of these proteins increases via heterotropic allostery (CaKD < 1 μM). Because of the high number and micromolar concentrations of EF-hand CBPs in a cell, at any given time, allostery is required physiologically, allowing for (i) proper Ca2+ homeostasis and (ii) strict maintenance of Ca2+-signaling within a narrow dynamic range of free Ca2+ ion concentrations, [Ca2+]free. In this review, mechanisms of allostery are coalesced into an empirical "binding and functional folding (BFF)" physiological framework. At the molecular level, folding (F), binding and folding (BF), and BFF events include all atoms in the biomolecular complex under study. The BFF framework is introduced with two straightforward BFF types for proteins (type 1, concerted; type 2, stepwise) and considers how homologous and nonhomologous amino acid residues of CBPs and their effector protein(s) evolved to provide allosteric tightening of Ca2+ and simultaneously determine how specific and relatively promiscuous CBP-target complexes form as both are needed for proper cellular function.

How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation

Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from ¹⁵N relaxation and side-chain dynamics from ¹³C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.

Dry Molten Globule-Like Intermediates in Protein Folding, Function, and Disease

The performance of a protein depends on its correct folding to the final functional native form. Hence, understanding the process of protein folding has remained an important field of research for the scientific community for the past five decades. Two important intermediate states, namely, wet molten globule (WMG) and dry molten globule (DMG), have emerged as critical milestones during protein folding-unfolding reactions. While much has been discussed about WMGs as a common unfolding intermediate, the evidence for DMGs has remained elusive owing to their near-native features, which makes them difficult to probe using global structural probes. This Review puts together the available literature and new evidence on DMGs to give a broader perspective on the universality of DMGs and discuss their significance in protein folding, function, and disease.

Self-Effected Allosteric Coupling and Cooperativity in Hypoxic Response Regulation with Disordered Proteins

Hypersensitive regulation of cellular hypoxic response relies on cooperative displacement of one disordered protein (HIF-1α) by another disordered protein (CITED2) from the target in a negative feedback loop. Considering the weak intramolecule coupling in disordered proteins, the molecular mechanism of high cooperativity in the molecular displacement event remains elusive. Herein, we show that disordered proteins utilize a "self-effected allostery" mechanism to achieve high binding cooperativity. Different from the conventional allostery mechanisms shown by many structured or disordered proteins, this mechanism utilizes one part of the disordered protein as the effector to trigger the allosteric coupling and enhance the binding of the remaining part of the same disordered protein, contributing to high cooperativity of the displacement event. The conserved charge motif of CITED2 is the key determinant of the molecular displacement event by serving as the effector of allosteric coupling. Such self-effected allostery provides an efficient strategy to achieve high cooperativity in the molecular events involving disordered proteins.

Dynamic allostery in substrate binding by human thymidylate synthase

Human thymidylate synthase (hTS) is essential for DNA replication and therefore a therapeutic target for cancer. Effective targeting requires knowledge of the mechanism(s) of regulation of this 72 kDa homodimeric enzyme. Here, we investigate the mechanism of binding cooperativity of the nucleotide substrate. We have employed exquisitely sensitive methyl-based CPMG and CEST NMR experiments enabling us to identify residues undergoing bifurcated linear 3-state exchange, including concerted switching between active and inactive conformations in the apo enzyme. The inactive state is populated to only ~1.3%, indicating that conformational selection contributes negligibly to the cooperativity. Instead, methyl rotation axis order parameters, determined by ²H transverse relaxation rates, suggest that rigidification of the enzyme upon substrate binding is responsible for the entropically-driven cooperativity. Lack of the rigidification in product binding and substrate binding to an N-terminally truncated enzyme, both non-cooperative, support this idea. In addition, the lack of this rigidification in the N-terminal truncation indicates that interactions between the flexible N-terminus and the rest of the protein, which are perturbed by substrate binding, play a significant role in the cooperativity—a novel mechanism of dynamic allostery. Together, these findings yield a rare depth of insight into the substrate binding cooperativity of an essential enzyme.

Decoding molecular recognition of inhibitors targeting HDAC2 via molecular dynamics simulations and configurational entropy estimation

Molecular recognition by enzymes is a complicated process involving thermodynamic energies governing protein-ligand interactions. In order to aid the estimation of inhibitory activity of compounds targeting an enzyme, several computational methods can be employed to dissect this intermolecular contact. Herein, we report a structural dynamics investigation of an epigenetic enzyme HDAC2 in differentiating its binding to various inhibitors within the sub-sites of its active site. Molecular dynamics (MD) simulation was employed to elucidate the intermolecular interactions as well as the dynamics behavior of ligand binding. MD trajectories of five distinct HDAC2-inhibitor complexes reveal that compounds lacking adequate contacts with the opening rim of the active site possess high fluctuation along the cap portion, thus weakening the overall affinity. Key intermolecular interactions determining the effective binding of inhibitors include hydrogen bonds with Gly154, Asp181, and Tyr308; hydrophobic interactions between Phe155/Phe210 and the linker region; and a pi-stacking with Arg39 at the foot pocket. Decomposition of the binding free energy calculated per-residue by MM/PBSA also indicates that the interactions within the internal foot pocket, especially with residues Met35, Leu144, Gly305, and Gly306, can contribute significantly to the ligand binding. Additionally, configurational entropy of the binding was estimated and compared to the scale of the binding free energy in order to assess its contribution to the binding and to differentiate various ligand partners. It was found that the levels of entropic contribution are comparable among a set of structurally similar carbamide ligands, while it is greatly different for the set of unrelated ligands, ranging from 2.75 to 16.38 kcal/mol for the five inhibitors examined. These findings exemplify the importance of assessing molecular dynamics as well as estimating the entropic contribution in evaluating the ligand binding mechanism.

Determination of immunogenic epitopes in major house dust mite allergen, Der p 2, via nanoallergens

BACKGROUND

Despite the high prevalence of allergic asthma, currently, avoidance of the responsible allergens, which is nearly impossible for allergens such as house dust mite (HDM), remains among the most effective treatment. Consequently, determination of the immunogenic epitopes of allergens will aid in developing a better understanding of the condition for diagnostic and therapeutic purposes. Current methods of epitope identification, however, only evaluate immunoglobulin E-epitope binding interactions, which is not directly related to epitope immunogenicity.

OBJECTIVE

To determine and rank the immunogenicity of the epitopes of major HDM allergen, Der p 2.

METHODS

We performed degranulation assays with RBL-SX38 cells primed using patient plasma and challenged with nanoallergens which multivalently displayed epitopes to study the relative immunogenicity of various epitopes of Der p 2. Nanoallergens were used to evaluate epitopes individually or in combination.

RESULTS

When evaluated using 3 patient samples, 3 epitopes in 2 distal regions of Der p 2 were identified as highly immunogenic when presented in combination, whereas no individual epitope triggered relevant degranulation. One of the epitopes (69-DPNACHYMKCPLVKGQQY-86) was identified to be cooperatively immunogenic when combined with other epitopes.

CONCLUSION

Our study highlights the importance of conformational epitopes in HDM-related allergies. This study also provides further evidence of the versatility of nanoallergens and their value for functional characterization of allergy epitopes, by ranking the Der p 2 epitopes according to immunogenicity. We believe that nanoallergens, by aiding in identification and understanding of immunogenic epitopes, will provide a better understanding of the manifestation of the allergic condition and potentially aid in developing new treatments.

M, Walker C, Kim J, Camilloni C, De Simone A, Vendruscolo M, Bernlohr DA, Taylor SS, Veglia G. ATP-competitive inhibitors modulate the substrate binding cooperativity of a kinase by altering its conformational entropy

ATP-competitive inhibitors are currently the largest class of clinically approved drugs for protein kinases. By targeting the ATP-binding pocket, these compounds block the catalytic activity, preventing substrate phosphorylation. A problem with these drugs, however, is that inhibited kinases may still recognize and bind downstream substrates, acting as scaffolds or binding hubs for signaling partners. Here, using protein kinase A as a model system, we show that chemically different ATP-competitive inhibitors modulate the substrate binding cooperativity by tuning the conformational entropy of the kinase and shifting the populations of its conformationally excited states. Since we found that binding cooperativity and conformational entropy of the enzyme are correlated, we propose a new paradigm for the discovery of ATP-competitive inhibitors, which is based on their ability to modulate the allosteric coupling between nucleotide and substrate-binding sites.

Exploring Glycan Binding Specificity of Odorranalectin by Alanine Scanning Library

Fluorescently labelled alanine scan analogues of odorranalectin (OL), a cyclic peptide that exhibits lectin like properties, were screened for binding BSA-conjugated monosaccharides using an enzyme-linked lectin assay (ELLA). Results revealed that Lys5, Phe7, Tyr9, Gly12, Leu14, and Thr17 were crucial for binding BSA-L-fucose, BSA-D-galactose and BSA-N-acetyl-D-galactosamine. Notably, Ala substitution of Ser3, Pro4, and Val13 resulted in higher binding affinities compared to the native OL. The obtained data also indicated that Arg8 plays an important role in differentiation of binding for BSA-L-fucose/D-galactose from BSA-N-acetyl-D-galactosamine. The thermodynamics of binding of the selected alanine analogues was evaluated by isothermal titration calorimetry. Low to moderate binding affinities were determined for the tetravalent MUC1 glycopeptide and asialofetuin, respectively, and high for the fucose rich polysaccharide, fucoidan. The thermodynamic profile of interactions with asialofetuin exhibits shift to an entropy-driven mechanism compared to the fucoidan, which displayed an enthalpyentropy compensation, typically associated with the carbohydratelectin recognition process.

Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India

Background

The massive increase in COVID-19 infection had generated a second wave in India during May–June 2021 with a critical pandemic situation. The Delta variant (B.1.617.2) was a significant factor during the second wave. Conversely, the UK had passed through the crucial phase of the pandemic from November to December 2020 due to B.1.1.7. The study tried to comprehend the pandemic response in the UK and India to the spread of the B.1.1.7 (Alpha, UK) variant and B.1.617.2 (Delta, India) variant.

Methods

This study was performed in three directions to understand the pandemic response of the two emerging variants. First, we served comparative genomics, such as genome sequence submission patterns, mutational landscapes, and structural landscapes of significant mutations (N501Y, D614G, L452R, E484Q, and P681R). Second, we performed evolutionary epidemiology using molecular phylogenetics, scatter plots of the cluster evaluation, country-wise transmission pattern, and frequency pattern. Third, the receptor binding pattern was analyzed using the Wuhan reference strain and the other two variants.

Results

The study analyzed the country-wise and region-wise genome sequences and their submission pattern, molecular phylogenetics, scatter plot of the cluster evaluation, country-wise geographical distribution and transmission pattern, frequency pattern, entropy diversity, and mutational landscape of the two variants. The structural pattern was analyzed in the N501Y, D614G L452R, E484Q, and P681R mutations. The study found increased molecular interactivity between hACE2-RBD binding of B.1.1.7 and B.1.617.2 compared to the Wuhan reference strain. Our receptor binding analysis showed a similar indication pattern for hACE2-RBD of these two variants. However, B.1.617.2 offers slightly better stability in the hACE2-RBD binding pattern through MD simulation than B.1.1.7.

Conclusion

The increased hACE2-RBD binding pattern of B.1.1.7 and B.1.617.2 might help to increase the infectivity compared to the Wuhan reference strain.

Entropies Derived from the Packing Geometries within a Single Protein Structure

A fast, simple, yet robust method to calculate protein entropy from a single protein structure is presented here. The focus is on the atomic packing details, which are calculated by combining Voronoi diagrams and Delaunay tessellations. Even though the method is simple, the entropies computed exhibit an extremely high correlation with the entropies previously derived by other methods based on quasi-harmonic motions, quantum mechanics, and molecular dynamics simulations. These packing-based entropies account directly for the local freedom and provide entropy for any individual protein structure that could be used to compute free energies directly during simulations for the generation of more reliable trajectories and also for better evaluations of modeled protein structures. Physico-chemical properties of amino acids are compared with these packing entropies to uncover the relationships with the entropies of different residue types. A public packing entropy web server is provided at packing-entropy.bb.iastate.edu, and the application programing interface is available within the PACKMAN (https://github.com/Pranavkhade/PACKMAN) package.

Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease

The three-dimensional conformations of a protein influence its function and select for the ligands it can interact with. The total free energy change during protein-ligand complex formation includes enthalphic and entropic components, which together report on the binding affinity and conformational states of the complex. However, determining the entropic contribution is computationally burdensome. Here, we apply kinematic flexibility analysis (KFA) to efficiently estimate vibrational frequencies from static protein and protein-ligand structures. The vibrational frequencies, in turn, determine the vibrational entropies of the structures and their complexes. Our estimates of the vibrational entropy change caused by ligand binding compare favorably to values obtained from a dynamic Normal Mode Analysis (NMA). Higher correlation factors can be achieved by increasing the distance cutoff in the potential energy model. Furthermore, we apply our new method to analyze the entropy changes of the SARS CoV-2 main protease when binding with different ligand inhibitors, which is relevant for the design of potential drugs.

Ligand binding remodels protein side-chain conformational heterogeneity

While protein conformational heterogeneity plays an important role in many aspects of biological function, including ligand binding, its impact has been difficult to quantify. Macromolecular X-ray diffraction is commonly interpreted with a static structure, but it can provide information on both the anharmonic and harmonic contributions to conformational heterogeneity. Here, through multiconformer modeling of time- and space-averaged electron density, we measure conformational heterogeneity of 743 stringently matched pairs of crystallographic datasets that reflect unbound/apo and ligand-bound/holo states. When comparing the conformational heterogeneity of side chains, we observe that when binding site residues become more rigid upon ligand binding, distant residues tend to become more flexible, especially in non-solvent-exposed regions. Among ligand properties, we observe increased protein flexibility as the number of hydrogen bonds decreases and relative hydrophobicity increases. Across a series of 13 inhibitor-bound structures of CDK2, we find that conformational heterogeneity is correlated with inhibitor features and identify how conformational changes propagate differences in conformational heterogeneity away from the binding site. Collectively, our findings agree with models emerging from nuclear magnetic resonance studies suggesting that residual side-chain entropy can modulate affinity and point to the need to integrate both static conformational changes and conformational heterogeneity in models of ligand binding.

Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization

The different niches through which bacteria move during their life cycle require a fast response to the many environmental queues they encounter. The sensing of these stimuli and their correct response is driven primarily by transcriptional regulators. This kind of protein is involved in sensing a wide array of chemical species, a process that ultimately leads to the regulation of gene transcription. The allosteric-coupling mechanism of sensing and regulation is a central aspect of biological systems and has become an important field of research during the last decades. In this review, we summarize the state-of-the-art techniques applied to unravel these complex mechanisms. We introduce a roadmap that may serve for experimental design, depending on the answers we seek and the initial information we have about the system of study. We also provide information on databases containing available structural information on each family of transcriptional regulators. Finally, we discuss the recent results of research about the allosteric mechanisms of sensing and regulation involving many transcriptional regulators of interest, highlighting multipronged strategies and novel experimental techniques. The aim of the experiments discussed here was to provide a better understanding at a molecular level of how bacteria adapt to the different environmental threats they face.

Electrostatic Interactions between CSTF2 and pre-mRNA Drive Cleavage and Polyadenylation

Nascent pre-mRNA 3'-end cleavage and polyadenylation (C/P) involves numerous proteins that recognize multiple RNA elements. Human CSTF2 binds to a downstream U- or G/U-rich sequence through its RNA recognition motif (RRM) regulating C/P. We previously reported the only known disease-related CSTF2 RRM mutant (CSTF2D50A) and showed that it changed the on-rate of RNA binding, leading to alternative polyadenylation in brains of mice carrying the same mutation. In this study, we further investigated the role of electrostatic interactions in the thermodynamics and kinetics of RNA binding for the CSTF2 RRM and the downstream consequences for regulation of C/P. By combining mutagenesis with NMR spectroscopy and biophysical assays, we confirmed that electrostatic attraction is the dominant factor in RRM binding to a naturally occurring U-rich RNA sequence. Moreover, we demonstrate that RNA binding is accompanied by an enthalpy-entropy compensation mechanism that is supported by changes in pico-to-nanosecond timescale RRM protein dynamics. We suggest that the dynamic binding of the RRM to U-rich RNA supports the diversity of sequences it encounters in the nucleus. Lastly, in vivo C/P assays demonstrate a competition between fast, high affinity RNA binding and efficient, correct C/P. These results highlight the importance of the surface charge of the RRM in RNA binding and the balance between nascent mRNA binding and C/P in vivo.

Entropy in the Molecular Recognition of Membrane Protein-Lipid Interactions

Understanding the molecular driving forces that underlie membrane protein-lipid interactions requires the characterization of their binding thermodynamics. Here, we employ variable-temperature native mass spectrometry to determine the thermodynamics of lipid binding events to the human G-protein-gated inward rectifier potassium channel, Kir3.2. The channel displays distinct thermodynamic strategies to engage phosphatidylinositol (PI) and phosphorylated forms thereof. The addition of a 4'-phosphate to PI results in an increase in favorable entropy. PI with two or more phosphates exhibits more complex binding, where lipids appear to bind two nonidentical sites on Kir3.2. Remarkably, the interaction of 4,5-bisphosphate PI with Kir3.2 is solely driven by a large, favorable change in entropy. Installment of a 3'-phosphate to PI(4,5)P2 results in an altered thermodynamic strategy. The acyl chain of the lipid has a marked impact on binding thermodynamics and, in some cases, enthalpy becomes favorable.

How Much Entropy Is Contained in NMR Relaxation Parameters?

Solution-state NMR relaxation experiments are the cornerstone to study internal protein dynamics at an atomic resolution on time scales that are faster than the overall rotational tumbling time τ_R. Since the motions described by NMR relaxation parameters are connected to thermodynamic quantities like conformational entropies, the question arises how much of the total entropy is contained within this tumbling time. Using all-atom molecular dynamics simulations of the T4 lysozyme, we found that entropy buildup is rather fast for the backbone, such that the majority of the entropy is indeed contained in the short-time dynamics. In contrast, the contribution of the slow dynamics of side chains on time scales beyond τ_R on the side-chain conformational entropy is significant and should be taken into account for the extraction of accurate thermodynamic properties.

Variable-Temperature Native Mass Spectrometry for Studies of Protein Folding, Stabilities, Assembly, and Molecular Interactions

The structures and conformational dynamics of proteins, protein complexes, and their noncovalent interactions with other molecules are controlled specifically by the Gibbs free energy (entropy and enthalpy) of the system. For some organisms, temperature is highly regulated, but the majority of biophysical studies are carried out at room, nonphysiological temperature. In this review, we describe variable-temperature electrospray ionization (vT-ESI) mass spectrometry (MS)-based studies with unparalleled sensitivity, dynamic range, and selectivity for studies of both cold- and heat-induced chemical processes. Such studies provide direct determinations of stabilities, reactivities, and thermodynamic measurements for native and non-native structures of proteins and protein complexes and for protein-ligand interactions. Highlighted in this review are vT-ESI-MS studies that reveal 40 different conformers of chymotrypsin inhibitor 2, a classic two-state (native → unfolded) unfolder, and thermochemistry for a model membrane protein system binding lipid and its regulatory protein. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy

The binding of small-molecule ligands to protein or nucleic acid targets is important to numerous biological processes. Accurate prediction of the binding modes between a ligand and a macromolecule is of fundamental importance in structure-based structure-function exploration. When multiple ligands with different sizes are docked to a target receptor, it is reasonable to assume that the residues in the binding pocket may adopt alternative conformations upon interacting with the different ligands. In addition, it has been suggested that the entropic contribution to binding can be important. However, only a few attempts to include the side chain conformational entropy upon binding within the application of flexible receptor docking methodology exist. Here, we propose a new physics-based scoring function that includes both enthalpic and entropic contributions upon binding by considering the conformational variability of the flexible side chains within the ensemble of docked poses. We also describe a novel hybrid searching algorithm that combines both molecular dynamics (MD)-based simulated annealing and genetic algorithm crossovers to address the enhanced sampling of the increased search space. We demonstrate improved accuracy in flexible cross-docking experiments compared with rigid cross-docking. We test our developments by considering five protein targets, thrombin, dihydrofolate reductase(DHFR), T4 L99A, T4 L99A/M102Q, and PDE10A, which belong to different enzyme classes with different binding pocket environments, as a representative set of diverse ligands and receptors. Each target contains dozens of different ligands bound to the same binding pocket. We also demonstrate that this flexible docking algorithm may be applicable to RNA docking with a representative riboswitch example. Our findings show significant improvements in top ranking accuracy across this set, with the largest improvement relative to rigid, 23.64%, occurring for ligands binding to DHFR. We then evaluate the ability to identify lead compounds among a large chemical space for the proposed flexible receptor docking algorithm using a subset of the DUD-E containing receptor targets MCR, GCR, and ANDR. We demonstrate that our new algorithms show improved performance in modeling flexible binding site residues compared to DOCK. Finally, we select the T4 L99A and T4 L99A/M102Q decoy sets, containing dozens of binders and experimentally validated nonbinders, to test our approach in distinguishing binders from nonbinders. We illustrate that our new algorithms for searching and scoring have superior performance to rigid receptor CDOCKER as well as AutoDock Vina. Finally, we suggest that flexible CDOCKER is sufficiently fast to be utilized in high-throughput docking screens in the context of hierarchical approaches.

Computational Design of Structured and Functional Peptide Macrocycles

Structure-based computational design methods have been developed to create proteins in silico with diverse shapes and sizes that accurately fold in vitro, from 7-residue macrocycles to megadalton-scale self-assembling nanomaterials. Precise control over protein shape has further enabled design and optimization of functional therapeutic proteins, including agonists, antagonists, enzymes, and vaccines. Computational design of functional peptides of smaller size presents a persistent challenge, with few successful examples to date. Herein we describe validated general methods for computational design of peptides using the Rosetta molecular modeling suite and discuss outstanding challenges and future directions.