CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca(2+)-ATPase

Absolute and Relative Binding Free Energy Calculations of Nucleotides to Multiple Protein Classes

Polyphosphate nucleotides, such as ATP, ADP, GTP, and GDP, play a crucial role in modulating protein functions through binding and/or catalytically activating proteins (enzymes). However, accurately calculating the binding free energies for these charged and flexible ligands poses challenges due to slow conformational relaxation and the limitations of force fields. In this study, we examine the accuracy and reliability of alchemical free energy simulations with fixed-charge force fields for the binding of four nucleotides to nine proteins of various classes, including kinases, ATPases, and GTPases. Our results indicate that the alchemical simulations effectively reproduce experimental binding free energies for all proteins that do not undergo significant conformational changes between their triphosphate nucleotide-bound and diphosphate nucleotide-bound states, with 87.5% (7 out of 8) of the absolute binding free energy results for 4 proteins within ±2 kcal/mol of experimental values and 88.9% (8 out of 9) of the relative binding free energy results for 9 proteins within ±3 kcal/mol of experimental values. However, our calculations show significant inaccuracies when divalent ions are included, suggesting that nonpolarizable force fields may not accurately capture interactions involving these ions. Additionally, the presence of highly charged and flexible ligands necessitates extensive conformational sampling to account for the long relaxation times associated with long-range electrostatic interactions. The simulation strategy presented here, along with its demonstrated accuracy across multiple protein classes, will be valuable for predicting the binding of nucleotides or their analogs to protein targets.

Development of Accurate Force Fields for Mg2+ and Triphosphate Interactions in ATP·Mg2+ and GTP·Mg2+ Complexes

In cells, adenosine triphosphate (ATP) and guanosine triphosphate (GTP) molecules typically form tricoordinated or bicoordinated ATP·Mg2+ or GTP·Mg2+ complexes with Mg2+ ions and bind to proteins, participating in and regulating many important cellular functions. The accuracy of their force field parameters plays a crucial role in studying the function-related conformations of ATP·Mg2+ or GTP·Mg2+ using molecular dynamics (MD) simulations. The parameters developed based on the methyl triphosphate model in existing AMBER force fields cannot accurately describe the conformational distribution of tricoordinated or bicoordinated ATP·Mg2+ or GTP·Mg2+ complexes in solution. In this study, we develop force field parameters for the triphosphate group based on the new ribosyl triphosphate model, considering the dihedral coupling effect, accurate van der Waals (vdW) interactions, and the influence of strongly polarized charges on conformational balance. The new force fields can accurately describe the conformational balance of tricoordinated and bicoordinated ATP·Mg2+ or GTP·Mg2+ conformations in solution and can be applied to simulate biological systems containing ATP·Mg2+ or GTP·Mg2+ complexes.

The tilting motion of the central core reveals the transport mechanism of the sarco/endoplasmic reticulum Ca2+-ATPase

The sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions per ATP hydrolyzed from the cytoplasm to the lumen. However, how the ATP hydrolysis remotely drives the Ca2+ transport is unclear. In the SERCA1a crystal structures, the ATP hydrolysis is accompanied by the notably increasing tilting angle of the central core (CC) and the Ca2+ transport, and the CC tilting angle dramatically decreases in the E2 to E1 transition. We demonstrated that the significantly increasing tilting motion of the CC drove the Ca2+ release in the molecular dynamics simulation of the R836A variant, and the dramatic spontaneous decrease in the CC tilting angle of the E2 state triggers the restart of the SERCA1a's transport cycle. The repulsion between the phosphorylated D351 and the phosphate groups in ADP triggers the release of ADP from the SERCA1a headpiece. We proposed a novel SERCA transport mechanism in which ATP hydrolysis drives a significant tilting motion of the CC, which drives Ca2+ transport and the A domain rotational motion in the E1P-ADP-2Ca2+ to E2P transition. The dramatic spontaneous decrease in the CC tilting angle of the E2 state drives the restart of the transport cycle.

Significance of Zn2+ in RyR1 for Structural Integrity and Ligand Binding: Insight from Molecular Dynamics

Ryanodine receptor type 1 (RyR1) is a Ca2+-release channel central to skeletal muscle excitation-contraction (EC) coupling. RyR1's cryo-EM structures reveal a zinc-finger motif positioned within the cytoplasmic C-terminal domain (CTD). Yet, owing to limitations in cryo-EM resolution, RyR1 structures lack precision in detailing the metal coordination structure, prompting the need for an accurate model. In this study, we employed molecular dynamics (MD) simulations and the density functional theory (DFT) method to refine the binding characteristics of Zn2+ in the zinc-finger site of the RyR1 channel. Our findings also highlight substantial conformational changes in simulations conducted in the absence of Zn2+. Notably, we observed a loss of contact at the interface between protein domains proximal to the zinc-finger site, indicating a crucial role of Zn2+ in maintaining structural integrity and interdomain interactions within RyR1. Furthermore, this study provides valuable insights into the modulation of ATP, Ca2+, and caffeine binding, shedding light on the intricate relationship between Zn2+ coordination and the dynamic behavior of RyR1. Our integrative approach combining MD simulations and DFT calculations enhances our understanding of the molecular mechanisms governing ligand binding in RyR1.

Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes

Molecular mechanics (MM) simulations have the potential to provide detailed insights into the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities of these enzymes also require the binding of divalent cations to catalytic sites. However, modeling divalent cations in MM simulations has been challenging. The inclusion of explicit polarization was considered promising, but despite improvements over nonpolarizable force fields and despite the inclusion of "Nonbonded-fix (NB-fix)" corrections, errors in interaction energies of divalent cations with proteins remain large. Importantly, the application of these models fails to reproduce the experimental structural data on Mg2+·Protein·ATP complexes. Focusing on these complexes, here we provide a systematic assessment of the polarizable AMOEBA model and recommend critical changes that substantially improve its predictive performance. Our key results are as follows. We first show that our recent revision of the AMOEBA protein model (AMOEBABIO18-HFC), which contains high field corrections (HFCs) to induced dipoles, dramatically improves Mg2+-protein interaction energies, reducing the mean absolute error (MAE) from 17 to 10 kcal/mol. This further supports the general applicability of AMOEBABIO18-HFC. The inclusion of many-body NB-fix corrections further reduces MAE to 6 kcal/mol, which amounts to less than 2% error. The errors are estimated with respect to vdW-inclusive density functional theory that we benchmark against CCSD(T) calculations and experiments. We also present a new model of ATP with revised polarization parameters to better capture its high field response, as well as new vdW and dihedral parameters. The ATP model accurately predicts experimental Mg2+-ATP binding free energy in the aqueous phase and provides new insights into how Mg2+ associates with ATP. Finally, we show that molecular dynamics (MD) simulations of Mg2+·Kinase·ATP complexes carried out with these improvements lead to a better agreement in global and local catalytic site structures between MD and X-ray crystallography.

An inorganic mineral-based protocell with prebiotic radiation fitness

Protocell fitness under extreme prebiotic conditions is critical in understanding the origin of life. However, little is known about protocell's survival and fitness under prebiotic radiations. Here we present a radioresistant protocell model based on assembly of two types of coacervate droplets, which are formed through interactions of inorganic polyphosphate (polyP) with divalent metal cation and cationic tripeptide, respectively. Among the coacervate droplets, only the polyP-Mn droplet is radiotolerant and provides strong protection for recruited proteins. The radiosensitive polyP-tripeptide droplet sequestered with both proteins and DNA could be encapsulated inside the polyP-Mn droplet, and form into a compartmentalized protocell. The protocell protects the inner nucleoid-like condensate through efficient reactive oxygen species' scavenging capacity of intracellular nonenzymic antioxidants including Mn-phosphate and Mn-peptide. Our results demonstrate a radioresistant protocell model with redox reaction system in response to ionizing radiation, which might enable the protocell fitness to prebiotic radiation on the primitive Earth preceding the emergence of enzyme-based fitness. This protocell might also provide applications in synthetic biology as bioreactor or drug delivery system.

Structural Dynamics and Catalytic Mechanism of ATP13A2 (PARK9) from Simulations

ATP13A2 is a gene encoding a protein of the P5B subfamily of ATPases and is a PARK gene. Molecular defects of the gene are mainly associated with variations of Parkinson's disease (PD). Despite the established importance of the protein in regulating neuronal integrity, the three-dimensional structure of the protein currently remains unresolved crystallographically. We have modeled the structure and reactivity of the full-length protein in its E1-ATP state. Using molecular dynamics (MD), quantum cluster, and quantum mechanical/molecular mechanical (QM/MM) methods, we aimed at describing the main catalytic reaction, leading to the phosphorylation of Asp513. Our MD simulations suggest that two positively charged Mg²⁺ cations are present at the active site during the catalytic reaction, stabilizing a specific triphosphate binding mode. Using QM/MM calculations, we subsequently calculated the reaction profiles for the phosphoryl transfer step in the presence of one and two Mg²⁺ cations. The calculated barrier heights in both cases are found to be ∼12.5 and 7.5 kcal mol^-1, respectively. We elucidated details of the catalytically competent ATP conformation and the binding mode of the second Mg²⁺ cofactor. We also examined the role of the conserved Arg686 and Lys859 catalytic residues. We observed that by significantly lowering the barrier height of the ATP cleavage reaction, Arg686 had major effect on the reaction. The removal of Arg686 increased the barrier height for the ATP cleavage by more than 5.0 kcal mol^-1 while the removal of key electrostatic interactions created by Lys859 to the γ-phosphate and Asp513 destabilizes the reactant state. When missense mutations occur in close proximity to an active site residue, they can interfere with the barrier height of the reaction, which can halt the normal enzymatic rate of the protein. We also found large binding pockets in the full-length structure, including a transmembrane domain pocket, which is likely where the ATP13A2 cargo binds.

Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca2+-ATPase

Ion pumps (or P-type ATPases) are membrane proteins, which transport ions through biological membranes against a concentration gradient, a function essential for many biological processes, such as muscle contraction, neurotransmission, and metabolism. Molecular mechanisms underlying active ion transport by ion pumps have been investigated by biochemical experiments and high-resolution structure analyses. Here, the transition of sarcoplasmic reticulum Ca²⁺-ATPase upon dissociation of Ca²⁺ is investigated using atomistic molecular dynamics simulations. We find intermediate structures along the pathway are stabilized by transient interactions between A- and P-domains as well as lipid molecules in the transmembrane helices.

Sarcoplasmic reticulum (SR) Ca²⁺-ATPase transports two Ca²⁺ ions from the cytoplasm to the SR lumen against a large concentration gradient. X-ray crystallography has revealed the atomic structures of the protein before and after the dissociation of Ca²⁺, while biochemical studies have suggested the existence of intermediate states in the transition between E1P⋅ADP⋅2Ca²⁺ and E2P. Here, we explore the pathway and free energy profile of the transition using atomistic molecular dynamics simulations with the mean-force string method and umbrella sampling. The simulations suggest that a series of structural changes accompany the ordered dissociation of ADP, the A-domain rotation, and the rearrangement of the transmembrane (TM) helices. The luminal gate then opens to release Ca²⁺ ions toward the SR lumen. Intermediate structures on the pathway are stabilized by transient sidechain interactions between the A- and P-domains. Lipid molecules between TM helices play a key role in the stabilization. Free energy profiles of the transition assuming different protonation states suggest rapid exchanges between Ca²⁺ ions and protons when the Ca²⁺ ions are released toward the SR lumen.

ATP-Magnesium Coordination: Protein Structure-Based Force Field Evaluation and Corrections

In the numerous molecular recognition and catalytic processes across biochemistry involving adenosine triphosphate (ATP), the common bioactive form is its magnesium chelate, ATP·Mg2+. In aqueous solution, two chelation geometries predominate, distinguished by bidentate and tridentate Mg2+-phosphate coordination. These are approximately isoenergetic but separated by a high energy barrier. Force field-based atomistic simulation studies of this complex require an accurate representation of its structure and energetics. Here we focused on the energetics of ATP·Mg2+ coordination. Applying an enhanced sampling scheme to circumvent prohibitively slow sampling of transitions between coordination modes, we observed striking contradictions between Amber and CHARMM force field descriptions, most prominently in opposing predictions of the favored coordination mode. Through further configurational free energy calculations, conducted against a diverse set of ATP·Mg2+-protein complex structures to supplement otherwise limited experimental data, we quantified systematic biases for each force field. The force field calculations were strongly predictive of experimentally observed coordination modes, enabling additive corrections to the coordination free energy that deliver close agreement with experiment. We reassessed the applicability of the thus corrected force field descriptions of ATP·Mg2+ for biomolecular simulation and observed that, while the CHARMM parameters display an erroneous preference for overextended triphosphate configurations that will affect many common biomolecular simulation applications involving ATP, the force field energy landscapes broadly agree with experimental measurements of solution geometry and the distribution of ATP·Mg2+ structures found in the Protein Data Bank. Our force field evaluation and correction approach, based on maximizing consistency with the large and heterogeneous collection of structural information encoded in the PDB, should be broadly applicable to many other systems.

Discovering the chloride pathway in the CFTR channel

Cystic fibrosis (CF), a lethal monogenic disease, is caused by pathogenic variants of the CFTR chloride channel. The majority of CF mutations affect protein folding and stability leading overall to diminished apical anion conductance of epithelial cells. The recently published cryo-EM structures of full-length human and zebrafish CFTR provide a good model to gain insight into structure-function relationships of CFTR variants. Although, some of the structures were determined in the phosphorylated and ATP-bound active state, none of the static structures showed an open pathway for chloride permeation. Therefore, we performed molecular dynamics simulations to generate a conformational ensemble of the protein and used channel detecting algorithms to identify conformations with an opened channel. Our simulations indicate a main intracellular entry at TM4/6, a secondary pore at TM10/12, and a bottleneck region involving numerous amino acids from TM1, TM6, and TM12 in accordance with experiments. Since chloride ions entered the pathway in our equilibrium simulations, but did not traverse the bottleneck region, we performed metadynamics simulations, which revealed two possible exits. One of the chloride ions exits includes hydrophobic lipid tails that may explain the lipid-dependency of CFTR function. In summary, our in silico study provides a detailed description of a potential chloride channel pathway based on a recent cryo-EM structure and may help to understand the gating of the CFTR chloride channel, thus contributing to novel strategies to rescue dysfunctional mutants.

Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires

We report a mechanism of adenosine triphosphate (ATP) to cyclic adenosine monophosphate (cAMP) conversion by the mammalian type V adenylyl cyclase revealed in molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) simulations. We characterize a set of computationally derived enzyme-substrate (ES) structures showing an important role of coordination shells of magnesium ions in the solvent accessible active site. In the lowest energy ES conformation, the coordination shell of Mg_A²⁺ does not include the O_δ1 atom of the conserved Asp440 residue. Starting from this conformation, a one-step reaction mechanism is characterized that includes proton transfer from the ribose O^3'H^3' group in ATP to Asp440 via a shuttling water molecule concerted with P^A-O^3A bond cleavage and O^3'-P^A bond formation. The energy profile of this route is consistent with the observed reaction kinetics. The computed energy profiles initiated from higher energy ES complexes are characterized by larger energy expenses to complete the reaction. Consistent with experimental data, we show that the Asp440Ala mutant of the enzyme should exhibit a reduced but retained activity. All considered reaction pathways include proton wires from the O^3'H^3' group via shuttling water molecules.

Chemo-Mechanical Coupling in the Transport Cycle of a Heme ABC Transporter

The heme importer from pathogenic bacteria is a member of the ATP-binding cassette (ABC) transporter family, which uses the energy of ATP-binding and hydrolysis for extensive conformational changes. Previous studies have indicated that conformational changes after heme translocation are triggered by ATP-binding to nucleotide binding domains (NBDs) and then, in turn, induce conformational transitions of the transmembrane domains (TMDs). In this study, we applied a template-based iterative all-atom molecular dynamics (MD) simulation to predict the ATP-bound outward-facing conformation of the Burkholderia cenocepacia heme importer BhuUV-T. The resulting model showed a stable conformation of the TMD with the cytoplasmic gate in the closed state and the periplasmic gate in the open state. Furthermore, targeted MD simulation predicted the intermediate structure of an occluded form (Occ) with bound ATP, in which both ends of the heme translocation channel are closed. The MD simulation of the predicted Occ revealed that Ser147 on the ABC signature motifs (LSGG[Q/E]) of NBDs occasionally flips and loses the active conformation required for ATP-hydrolysis. The flipping motion was found to be coupled to the inter-NBD distance. Our results highlight the functional significance of the signature motif of ABC transporters in regulation of ATPase and chemo-mechanical coupling mechanism.

A change in structural integrity of c-Kit mutant D816V causes constitutive signaling

Several signaling pathways, ligands, and genes that regulate proliferative and self-renewal properties of the Hematopoietic Stem Cells (HSCs) have been studied meticulously. One of the signaling pathways that play a crucial role in the process of hematopoiesis is the Stem Cell Factor (SCF) mediated c-Kit pathway. The c-Kit is a Receptor Tyrosine Kinase (RTK), which is expressed in the cells including HSCs. It undergoes dimerization upon binding with its cognate ligand SCF. As a result, phosphorylation of the Juxtamembrane (JM) domain of c-Kit takes place at Tyr568 and Tyr570 residues. These phosphorylated residues become the docking sites for protein tyrosine phosphatases (PTPs) namely SHP-1 and SHP-2, which in turn cause dephosphorylation and negative regulation of the downstream signaling responsible for the cell proliferation. Interestingly, it has been reported that the mutation of c-Kit at D816V makes it independent of SCF stimulation and SHP-1/SHP-2 inhibition, thereby, causing its constitutive activation. The present study was commenced to elucidate the structural behavior of this mutation in the JM and A-loop region of c-Kit using Molecular Dynamics (MD) simulations of the wild-type and mutant c-Kit in unphosphorylated and phosphorylated states. The energy difference computed between the wild type and mutant (D816V) c-Kit, and protein-protein docking and complex analysis revealed the impact of this single residue mutation on the integrity dynamics of c-Kit that makes it independent of SHP-1/SHP-2 negative regulation.

Kinesin motility is driven by subdomain dynamics

The microtubule (MT)-associated motor protein kinesin utilizes its conserved ATPase head to achieve diverse motility characteristics. Despite considerable knowledge about how its ATPase activity and MT binding are coupled to the motility cycle, the atomic mechanism of the core events remain to be found. To obtain insights into the mechanism, we performed 38.5 microseconds of all-atom molecular dynamics simulations of kinesin-MT complexes in different nucleotide states. Local subdomain dynamics were found to be essential for nucleotide processing. Catalytic water molecules are dynamically organized by the switch domains of the nucleotide binding pocket while ATP is torsionally strained. Hydrolysis products are 'pulled' by switch-I, and a new ATP is 'captured' by a concerted motion of the α0/L5/switch-I trio. The dynamic and wet kinesin-MT interface is tuned for rapid interactions while maintaining specificity. The proposed mechanism provides the flexibility necessary for walking in the crowded cellular environment.

Motor proteins called kinesins perform a number of different roles inside cells, including transporting cargo and organizing filaments called microtubules to generate the force needed for a cell to divide. Kinesins move along the microtubules, with different kinesins moving in different ways: some ‘walk’, some jump, and some destroy the microtubule as they travel along it. All kinesins power their movements using the same molecule as fuel – adenosine triphosphate, known as ATP for short.

Energy stored in ATP is released by a chemical reaction known as hydrolysis, which uses water to break off specific parts of the ATP molecule. The site to which ATP binds in a kinesin has a similar structure to the ATP binding site of many other proteins that use ATP. However, little was known about the way in which kinesin uses ATP as a fuel, including how ATP binds to kinesin and is hydrolyzed, and how the products of hydrolysis are released. These events are used to power the motor protein.

Hwang et al. have used powerful computer simulation methods to examine in detail how ATP interacts with kinesin whilst moving across a microtubule. The simulations suggest that regions (or 'domains') of kinesin near the ATP binding site move around to help in processing ATP. These kinesin domains trap a nearby ATP molecule from the environment and help to deliver water molecules to ATP for hydrolysis. Hwang et al. also found that the domain motion subsequently helps in the release of the hydrolysis products by kinesin.

The domains around the ATP pocket vary among the kinesins and these differences may enable kinesins to fine-tune how they use ATP to move. Further investigations will help us understand why different kinesin families behave differently. They will also contribute to exploring how kinesin inhibitors might be used as anti-cancer drugs.