Charles L Brooks

University of Michigan | U-M · Department of Chemistry

Multisite λ-dynamics (MSλD) is a novel method for the calculation of relative free energies of binding for ligands to their targeted receptors. It can be readily used to examine a large number of molecules with multiple functional groups at multiple sites around a common core. This makes MSλD a powerful tool in structure-based drug design. In the p...

The coactivator KIX of CBP uses two binding surfaces to recognize multiple activators and exhibits allostery in ternary complex formation. Activator•coactivator interactions are central to transcriptional regulation, yet the microscopic origins of allostery in dynamic proteins like KIX are largely unknown. Here, we investigate the molecular recogni...

Inhibitors of transcriptional protein-protein interactions (PPIs) have high value both as tools and for therapeutic applications. The PPI network mediated by the transcriptional coactivator Med25, for example, regulates stress-response and motility pathways, and dysregulation of the PPI networks contributes to oncogenesis and metastasis. The canoni...

Computation of the thermodynamic consequences of protein mutations holds great promise in protein biophysics and design. Alchemical free energy methods can give improved estimates of mutational free energies, and are already widely used in calculations of relative and absolute binding free energies in small molecule design problems. In principle, a...

Inhibitors of transcriptional protein-protein interactions (PPIs) have high value both as tools and for therapeutic applications. The PPI network mediated by the transcriptional coactivator Med25, for example, regulates stress-response and motility pathways and dysregulation of the PPI networks contributes to oncogenesis and metastasis. The canonic...

The COVID-19 pandemic has highlighted the need for new antiviral targets, as many of the currently approved drugs have proven ineffective against mitigating SARS-CoV-2 infections. The host transmembrane serine protease TMPRSS2 is a highly promising antiviral target, as it plays a direct role in priming the spike protein before viral entry occurs. F...

Accurate predictions of changes to protein-ligand binding affinity in response to chemical modifications are of utility in small-molecule lead optimization. Relative free-energy perturbation (FEP) approaches are one of the most widely utilized for this goal but involve significant computational cost, thus limiting their application to small sets of...

When the electrostatic environment surrounding binding partners changes between unbound and bound states, the net uptake or release of a proton is possible by either binding partner. This process is pH-dependent in that the free energy required to uptake or release the proton varies with pH. This pH-dependence is typically not considered in convent...

Fast Fourier transform (FFT)-based protein ligand docking together with parallel simulated flexible ligand - flexible receptor docking are implemented on GPU- accelerated platforms to significantly enhance the throughput of the CDOCKER and Flexible CDOCKER docking algorithms in the CHARMM program for biomolecule modeling. The FFT-based approach for...

The transcriptional adaptor zinc-binding 1 (TAZ1) domain of the transcriptional coactivator CBP/P300 and two disor-dered peptides HIF-1α and CITED2 form a delicate protein switch that regulates cellular hypoxic response. In hypoxia, HIF-1α binds TAZ1 to control the transcription of adaptive genes critical for the recovery from hypoxic stress. CITED...

The generalized Born with molecular volume and solvent accessible surface area (GBMV2/SA) implicit solvent model provides an accurate description of molecular volume and has the potential to accurately describe the conformational equilibria of structured and disordered proteins. However, its broader application has been limited by the computational...

Alchemical free energy calculations have made a dramatic impact upon the field of structure-based drug design by allowing functional group modifications to be explored computationally prior to experimental synthesis and assay evaluation, thereby informing and directing synthetic strategies. In furthering the advancement of this area, a series of 21...

Significance The ways in which proteins fold to their native state remain a challenging and important question in biology. Large proteins often populate meta-stable intermediate states before reaching their native conformation, making them excellent targets for understanding the sequence-structure code. We studied folding of indole-3-glycerol phosp...

Single layered two-dimensional (2D) materials such as transition metal dichalcogenides (TMDs) showed great potential in many microelectronic or nanoelectronic applications. For example, because of its extremely high sensitivity, TMDs-based biosensor becomes a promising candidate for the next generation label-free detection. However, very few studie...

The multistate Bennett acceptance ratio method (MBAR) and unbinned weighted histogram analysis method (UWHAM) are widely employed approaches to calculate relative free energies of multiple thermodynamic states that gain statistical precision by employing free energy contributions from configurations sampled at each of the simu- lated λ state. With...

Immobilization on solid supports provides an effective way to improve enzyme stability and simplify downstream processing for biotechnological applications, which has been widely used in research and in applications. However, surface immobilization may disrupt enzyme structure due to interactions between the enzyme and the supporting substrate, lea...

Numerous classes of riboswitches have been found to regulate bacterial gene expression in response to physiological cues, offering new paths to antibacterial drugs. As common studies of isolated riboswitches lack the functional context of the transcription machinery, we here combine single-molecule, biochemical, and simulation approaches to investi...

The VIrus Particle ExploreR database (VIPERdb) ( http://viperdb.scripps.edu ) is a database and web portal for primarily icosahedral virus capsid structures that integrates structure-derived information with visualization and analysis tools accessed through a set of web interfaces. Our aim in developing VIPERdb is to provide comprehensive structure...

The estimation of changes in free energy upon mutation is central to the problem of protein design. Modern protein design methods have had remarkable success over a wide range of design targets, but are reaching their limits in ligand binding and enzyme design due to insufficient accuracy in mutational free energies. Alchemical free energy calculat...

Significance Transcriptional coactivators and their partner transcription factors have been labeled as intrinsically disordered, fuzzy, and undruggable. We propose that the identification of conserved mechanisms of engagement between coactivators and their cognate activators should provide general principles for small-molecule modulator discovery....

In this study, we demonstrate the extensive scalability of the biasing potential replica exchange multisite λ-dynamics (BP-REX MSλD) free energy method by calculating binding affinities for 512 inhibitors to HIV Reverse Transcriptase (HIV-RT). This is the largest exploration of chemical space using free energy methods known to date, requires only a...

Tethering peptides and proteins to abiotic surfaces has the potential to create biomolecule-functionalized surfaces with useful properties. Commonly used methods of immobilization lack control over the orientation in which biological molecules are covalently or physically bound to the surface, leading to sub-optimal materials. Here we use an engine...

Two-dimensional (2D) materials such as graphene, molybdenum disulfide (MoS2), tungsten diselenide (WSe2), and black phosphorous are being developed for sensing applications with excellent selectivity and high sensitivity. In such applications, 2D materials extensively interact with various analytes including biological molecules. Understanding inte...

The opportunity to prospectively predict ligand bound poses and free energies of binding to the Farnesoid X Receptor in the D3R Grand Challenge 2 provided a useful exercise to evaluate CHARMM based docking (CDOCKER) and [Formula: see text]-dynamics methodologies for use in "real-world" applications in computer aided drug design. In addition to meas...

λ-dynamics is a generalized ensemble method for alchemical free energy calcula- tions. In traditional λ-dynamics, the alchemical switch variable λ is treated as a continuous variable ranging from 0 to 1 and an empirical estimator (∆Gˆ = -β(-1)ln[P(λ > λcutoff)/P (λ < 1-λcutoff)]) is utilized to approximate the free energy (∆G = -β(-1)ln[P (λ = 1)/P...

Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various f...

The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with biophysical processes, and when combined with coarse-grained simulations, can be particularly useful for accounting for...

Understanding the fundamental biophysics behind protein-nanoparticle (NP) interactions is essential for the design and engineering bio-NP systems. The authors describe the development of a coarse-grained protein-NP model that utilizes a structure centric protein model. A key feature of the protein-NP model is the quantitative inclusion of the hydro...

Multisite dynamics (MS D) is a powerful emerging method in free energy calculation that allows prediction of relative free energies for a large set of compounds from very few simulations. Calculating free energy differences between substituents that constitute large volume or flexibility jumps in chemical space is difficult for free energy methods...

Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applicati...

Post-translational S-palmitoylation directs the trafficking and membrane localization of hundreds of cellular proteins, often involving a coordinated palmitoylation cycle that requires both protein acyl transferases (PATs) and acyl protein thioesterases (APTs) to actively re-distribute S-palmitoylated proteins towards different cellular membrane co...

Aberrant canonical NF-κB signaling is implicated in diseases from autoimmune disorders to cancer. A major therapeutic challenge is the need for selective inhibition of the canonical pathway without impacting the many non-canonical NF-κB functions. Here we show that a selective peptide-based inhibitor of canonical NF-κB signaling, in which a hydroge...

Aberrant canonical NF-κB signaling is implicated in diseases from autoimmune disorders to cancer. A major therapeutic challenge is the need for selective inhibition of the canonical pathway without impacting the many non-canonical NF-κB functions. Here we show that a selective peptide-based inhibitor of canonical NF-κB signaling, in which a hydroge...

Antimicrobial peptides (AMPs), due to their unique structure/function relationship, have great potential to be developed into novel diagnostic and therapeutic agents for a variety of pathogens and illnesses. Often such peptides are administered using powder or suspension, limiting their reusability or recyclability. Immobilization of these antimicr...

Chaperones maintain a healthy proteome by preventing aggregation and by aiding in protein folding. Precisely how chaperones influence the conformational properties of their substrates, however, remains unclear. To achieve a detailed description of dynamic chaperone-substrate interactions, we fused site-specific NMR information with coarse-grained s...

The treatment of pH sensitive ionization states for titratable residues in proteins is often omitted from molecular dynamics (MD) simulations. While static charge models can answer many questions regarding protein conformational equilibrium and protein-ligand interactions, pH-sensitive phenomena such as acid-activated chaperones and amyloidogenic p...

A halogen bond is a highly directional, non-covalent interaction between a halogen atom and another electronegative atom. It arises due to the formation of a small region of positive electrostatic potential opposite the covalent bond to the halogen, called the ‘sigma hole.’ Empirical force fields in which the electrostatic interactions are represen...

Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how c...

The hairpin ribozyme is an RNA enzyme found in plant viruses that catalyzes cleavage and ligation reactions in RNA replication. The active site is formed when two loop domains located on separate helical arms are in contact. We conduct coarse-grained molecular dynamics simulations of the hairpin ribozyme using the TOPRNA model. By modifying the top...

Molecular chaperones interact with unfolded proteins to prevent aberrant folding and aggregation in the crowded cellular milieu. Despite their critical role in maintaining protein homeostasis, achieving detailed models of the highly dynamic interaction between a chaperone and an unfolded substrate has proven to be a difficult task. We address this...

Many experimental and theoretical methods have been developed to calculate the coarse-grained continuum elastic properties of macromolecules. However, all of those methods assume uniform elastic properties. Following the continuum mechanics framework, we present a systematic way of calculating the nonuniform effective elastic properties from atomic...

Two fundamental challenges of simulating biologically relevant systems are the rapid calculation of the energy of solvation and the trajectory length of a given simulation. The Generalized Born model with a Simple sWitching function (GBSW) addresses these issues by using an efficient approximation of Poisson-Boltzmann (PB) theory to calculate each...

Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols us...

A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynami...

Significance Calreticulin mutants that disrupt ATP binding are shown to prolong cellular MHC class I interactions with calreticulin and with the transporter associated with antigen processing (TAP). To our knowledge, no previous studies have implicated a role for endoplasmic reticulum (ER) luminal ATP as a determinant of MHC class I assembly comple...

Intrinsically disordered regions of proteins can gain structure by binding to a partner. This process, of coupled folding and binding (CFaB), is a fundamental part of many important biological processes. Structure-based models have proven themselves capable of revealing fundamental aspects of how CFaB occurs, however, typical methods to enhance the...

Molecular dynamics (MD) simulation is a useful tool for simulating formulations of surfactant mixtures from first principles, which can be used to predict surfactant morphology and other industrially-relevant thermodynamic properties. However, the surfactant structure is sensitive to the parameters used in MD simulations, and in the absence of exte...

Mammalian mitochondrial tRNASer(UCN) (mt-tRNASer) and pyrrolysine tRNA (tRNAPyl) fold to near-canonical three-dimensional structures despite having non-canonical secondary structures with shortened interhelical loops that disrupt the conserved tRNA tertiary interaction network. How these non-canonical tRNAs compensate for their loss of tertiary int...

Traditional free energy calculation methods are well known for their drawbacks in scalability and speed in converging results particularly for calculations with large perturbations. Here, we report on the development of biasing potential replica exchange multi-site ?-dynamics (BP-REX MS?D), which is a free energy method that is capable of performin...

A recently engineered mutant of cyan fluorescent protein (WasCFP) that exhibits pH-dependent absorption suggests that its tryptophan-based chromophore switches between neutral (protonated) and charged (deprotonated) states depending on external pH. At pH 8.1 the latter gives rise to green fluorescence as opposed to the cyan color of emission that i...

Significance Alphaviruses infect human cells through endocytosis and low pH-triggered membrane fusion. Because of the recent epidemics and lack of specific treatment for alphaviral infections, numerous investigations have aimed to deduce the mechanism of the alphaviral infection pathway. Building on previous structural models of the viral envelope...

The bacterial acid stress-sensing chaperone HdeA loses structure to gain function. As enteropathogenic E. coli pass through the severely acidic environment of the mammalian stomach, HdeA transitions from an inactive, folded dimer to chaperone-active, unfolded monomers to protect against the acid-induced aggregation of periplasmic proteins. Toward a...

Given the demonstrated utility of coarse-grained modeling and simulations approaches in studying protein structure and dynamics, developing methods that allow experimental observables to be directly recovered from coarse-grained models is of great importance. In this work, we develop one such method that enables protein backbone chemical shifts ((1...

The pH-sensing chaperone HdeA promotes the survival of enteropathogenic bacteria during transit through the harshly acidic environment of the mammalian stomach. At low pH, HdeA transitions from an inactive, folded, dimer to chaperone-active, disordered, monomers to protect against the acid-induced aggregation of periplasmic proteins. Toward achievi...

The propensity of backbone Cα atoms to engage in carbon-oxygen (CH⋯O) hydrogen bonding is well-appreciated in protein structure, but side chain CH⋯O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH⋯O hydrogen bonding is examined through a survey of neutron crystal structure...

HIV-1 TAR RNA is a two-helix bulge motif that plays a critical role in HIV viral replication and is an important drug target. However, efforts at designing TAR inhibitors have been challenged by its high degree of structural flexibility, which includes slow large-amplitude reorientations of its helices with respect to one another. Here, we use the...

Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained mol...

Significance Folding mechanisms of large proteins are often complicated by the existence of kinetic traps that impede progress toward the native conformation. We have tested the role of chain connectivity in creating such traps by permuting the sequence of a small α/β/α sandwich protein, the chemotaxis response regulator Y. An approach combining ex...

The role of pH in regulating biological activity is ubiquitous, and our understanding of pH-mediated activity has traditionally relied on analyzing static biomolecular structures of highly populated ground states solved near physiological pH. However, recent advances have demonstrated the increasing importance of transiently populated states, which...

Cytoplasmic osmolytes can significantly alter the thermodynamic and kinetic properties of proteins relative to those in dilute solution conditions. Spectroscopic experiments of lysozymes in cosolvents indicate that such changes may arise from the heterogeneous, site-specific hydrophobic interactions between protein surface residues and individual s...

Ribosomes control the missense error rate of ~10(-4) during translation though quantitative contributions of individual mechanistic steps of the conformational changes yet to be fully determined. Biochemical and biophysical studies led to a qualitative tRNA selection model in which ribosomal A-site residues A1492 and A1493 (A1492/3) flip out in res...

RNA dynamics play a fundamental role in many cellular functions. However, there is no general framework to describe these complex processes, which typically consist of many structural maneuvers that occur over timescales ranging from picoseconds to seconds. Here, we classify RNA dynamics into distinct modes representing transitions between basins o...