Conformation Of Binding Site Research Articles

Structural and Dynamic Effects Due to Glycation on Cholinesterases

Diabetes mellitus is one of the most common diseases in the world. Currently around 3% of the global population suffers from diabetes and this is expected to double by 2030. During hyperglycemic episodes, protein glycation may occur on lysine residues. Decrease of biological activity as a direct effect of glycation has been shown on calmodulin, superoxide dismutase and calcium ATPase on human erythrocytes. In this work, we evaluated the structural and dynamical effects due to lysine glycation on human acetylcholinesterase and butyrylcholinesterase. Four probable sites were tested and analyzed for each cholinesterase by molecular dynamics simulations, using the CHARMM27 forcefield in NAMD at 298K, for 25ns on each model. The cumulative effect of each site was studied comparing it to the native, unglycated protein structure. The structural and dynamic consequences due to lysine glycation on the conformation of the choline binding site are reported.Funding: Macroproyecto de Tecnologias de la Informacion y la Computacion (UNAM), Centro Nacional de Supercomputo (IPICYT), Supercomputadora Aitzaloa (UAM). Postdoctoral Funding (CONACYT).

Hydrophobic Binding Hot Spots of Bcl-xL Protein-Protein Interfaces by Cosolvent Molecular Dynamics Simulation.

Identifying binding hot spots in protein-protein interfaces is important for understanding the binding specificity and for the design of nonpeptide, small molecule inhibitors. Molecular dynamics simulation in the isopropanol/water cosolvent environment and in water was employed to investigate Bcl-xL protein, which has a highly flexible, large, and primarily hydrophobic binding site. Simulations of either the apo- or holocrystal structures of the Bcl-xL in pure water fail to generate conformations found in the cocrystal structures of Bcl-xL in complex with its binding partners due to hydrophobic collapse. In contrast, simulations in cosolvent starting either from the apo- or holocrystal structure of the Bcl-xL yield binding-site conformations similar to that found in the cocrystal structures of Bcl-xL. Hydrophobic binding hot spots identified using the conformations from the cosolvent simulations are in excellent agreement with experimental structural data of known inhibitors. Importantly, cosolvent simulations revealed the highly dynamic nature of the hydrophobic binding pockets in Bcl-xL and yielded new structural insights for the design of novel Bcl-xL small-molecule inhibitors.

The HIV Type 1 Protease L10I Minor Mutation Decreases Replication Capacity and Confers Resistance to Protease Inhibitors

The effect of minor mutations in PR on treatment outcome has not been well established. We characterized the HIV protease minor mutations, L10I, compared to the minor mutation, L63P, and the major mutation D30N and their impact on viral fitness and resistance to protease inhibitors. Mutations were introduced individually and in combination by site-directed mutagenesis into the provirus pNL4.3ren and constructs used for replication capacity (RC) and resistance assays. A structure prediction of the protease carrying the L10I mutation was determined. The prevalence of the minor mutation L10I had a pattern similar to that found for major mutations D30N, with a low prevalence (4.9%) in naive patients and significantly higher prevalence in treated patients. Furthermore, viruses carrying the major mutation D30N or the minor mutation L10I showed a significant decrease in RC (p-value <0.05), whereas viruses carrying the minor mutation L63P had RC similar to wild-type virus. In addition, the L10I mutation conferred resistance to saquinavir, which was supported by the higher prevalence in the cohort of the L10I mutation among patients with SQV resistance. The molecular modeling suggests that L10I may affect the conformation of Leu-23, a critical residue in the substrate binding site. In conclusion, the L10I mutation impairs RC and confers resistance to SQV, similarly to other major mutations, which may be related with changes in the conformation in the protease binding site. The presence of this mutation in the genotype of HIV from patients should be taken into consideration when designing new optimize treatments.

TPC2 Is a Novel NAADP-sensitive Ca2+ Release Channel, Operating as a Dual Sensor of Luminal pH and Ca2+

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a molecule capable of initiating the release of intracellular Ca2+ required for many essential cellular processes. Recent evidence links two-pore channels (TPCs) with NAADP-induced release of Ca2+ from lysosome-like acidic organelles; however, there has been no direct demonstration that TPCs can act as NAADP-sensitive Ca2+ release channels. Controversial evidence also proposes ryanodine receptors as the primary target of NAADP. We show that TPC2, the major lysosomal targeted isoform, is a cation channel with selectivity for Ca2+ that will enable it to act as a Ca2+ release channel in the cellular environment. NAADP opens TPC2 channels in a concentration-dependent manner, binding to high affinity activation and low affinity inhibition sites. At the core of this process is the luminal environment of the channel. The sensitivity of TPC2 to NAADP is steeply dependent on the luminal [Ca2+] allowing extremely low levels of NAADP to open the channel. In parallel, luminal pH controls NAADP affinity for TPC2 by switching from reversible activation of TPC2 at low pH to irreversible activation at neutral pH. Further evidence earmarking TPCs as the likely pathway for NAADP-induced intracellular Ca2+ release is obtained from the use of Ned-19, the selective blocker of cellular NAADP-induced Ca2+ release. Ned-19 antagonizes NAADP-activation of TPC2 in a non-competitive manner at 1 μm but potentiates NAADP activation at nanomolar concentrations. This single-channel study provides a long awaited molecular basis for the peculiar mechanistic features of NAADP signaling and a framework for understanding how NAADP can mediate key physiological events.

Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases

The microscopic mechanism of coupled c-ring rotation and ion translocation in F(1)F(o)-ATP synthases is unknown. Here we present conclusive evidence supporting the notion that the ability of c-rings to rotate within the F(o) complex derives from the interplay between the ion-binding sites and their nonhomogenous microenvironment. This evidence rests on three atomic structures of the c(15) rotor from crystals grown at low pH, soaked at high pH and, after N,N'-dicyclohexylcarbodiimide (DCCD) modification, resolved at 1.8, 3.0 and 2.2 Å, respectively. Alongside a quantitative DCCD-labeling assay and free-energy molecular dynamics calculations, these data demonstrate how the thermodynamic stability of the so-called proton-locked state is maximized by the lipid membrane. By contrast, a hydrophilic environment at the a-subunit-c-ring interface appears to unlock the binding-site conformation and promotes proton exchange with the surrounding solution. Rotation thus occurs as c-subunits stochastically alternate between these environments, directionally biased by the electrochemical transmembrane gradient.

Homology-Modelling Protein–Ligand Interactions: Allowing for Ligand-Induced Conformational Change

Current homology-modelling methods do not consider small molecules in their automated processes. Therefore, the development of a reliable tool for protein–ligand homology modelling is an important next step in generating plausible models for molecular interactions. Two automated protein–ligand homology-modelling strategies, requiring no expert knowledge from the user, are investigated here. Both employ the “induced fit” concept with flexibility in side chains and ligand. The most successful strategy superimposes the new ligand over the original ligand before homology modelling, allowing the new ligand to be taken into consideration during protein modelling (rather than after), facilitating conformational change in the local backbone if necessary. We show that this approach results in successful modelling of the ligand and key binding-site residues of angiotensin-converting enzyme 2 (ACE2) from its homologue ACE, which is not possible via conventional homology modelling or by homology modelling followed by docking. Several other difficult target complexes are also successfully modelled, reproducing native protein–ligand contacts with significantly different biological substrates and different binding-site conformations. These include the modelling of Cdk5 (cyclin-dependent kinase 5) from Cdk2, thymidine phosphorylase from a bacterial homologue, and dihydrofolate reductase from a recombinant variant with a markedly different inhibitor. In terms of average modelling quality across 82 targets, the ligand RMSD with respect to the experimental structure is 1.4 Å (and 2.0 Å for the protein binding site) for “easy” cases and 2.9 Å for the ligand (and 2.7 Å for the protein binding site) in “hard” cases. This demonstrates the importance of selecting an optimal template. Ligand-modelling accuracy is strongly dependent on target–template ligand structural similarity, rather than target–template sequence identity. However, protein-modelling accuracy is dependent on both. Our automated protein–ligand homology-modelling strategy generates a higher degree of accuracy than homology modelling followed by docking, generating an average ligand RMSD that is 1–2 Å better than docking with homology models.

Computational characterization of how the VX nerve agent binds human serum paraoxonase 1

Human serum paraoxonase 1 (HuPON1) is an enzyme that can hydrolyze various chemical warfare nerve agents including VX. A previous study has suggested that increasing HuPON1's VX hydrolysis activity one to two orders of magnitude would make the enzyme an effective countermeasure for in vivo use against VX. This study helps facilitate further engineering of HuPON1 for enhanced VX-hydrolase activity by computationally characterizing HuPON1's tertiary structure and how HuPON1 binds VX. HuPON1's structure is first predicted through two homology modeling procedures. Docking is then performed using four separate methods, and the stability of each bound conformation is analyzed through molecular dynamics and solvated interaction energy calculations. The results show that VX's lone oxygen atom has a strong preference for forming a direct electrostatic interaction with HuPON1's active site calcium ion. Various HuPON1 residues are also detected that are in close proximity to VX and are therefore potential targets for future mutagenesis studies. These include E53, H115, N168, F222, N224, L240, D269, I291, F292, and V346. Additionally, D183 was found to have a predicted pKa near physiological pH. Given D183's location in HuPON1's active site, this residue could potentially act as a proton donor or accepter during hydrolysis. The results from the binding simulations also indicate that steered molecular dynamics can potentially be used to obtain accurate binding predictions even when starting with a closed conformation of a protein's binding or active site.

A flexible docking scheme to explore the binding selectivity of PDZ domains

Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using ROSETTALIGAND, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 A. We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately.

HMBA depolymerizes microtubules, activates mitotic checkpoints and induces mitotic block in MCF-7 cells by binding at the colchicine site in tubulin

10-[(3-Hydroxy-4-methoxybenzylidene)]-9(10H)-anthracenone (HMBA), a synthetic compound, has been reported to have a potent antitumor activity. In this study, we found that HMBA depolymerized microtubules in MCF-7 cells and produced aberrant spindles in the MCF-7 cells. It also reduced the distance between the centrosomes and activated the mitotic checkpoint proteins BubR1 and Mad2. Further, HMBA inhibited the progression of MCF-7 cells in mitosis and induced apoptotic cell death involving p53 pathway. In vitro, HMBA bound to purified brain tubulin with a dissociation constant of 4.1 ± 0.9 μM. It inhibited microtubule assembly and increased the GTP hydrolysis rate of microtubule assembly. The compound did not alter the binding of 2′(or 3′)- O-(trinitrophenyl) guanosine 5′-triphosphate (TNP–GTP), a fluorescent analogue of GTP, to tubulin suggesting that it did not inhibit the binding of GTP to tubulin. However, we obtained evidence indicating that HMBA perturbed the conformation of the GTP binding site in tubulin. In addition, an analysis of the modified Dixon plot suggested that HMBA competitively inhibited the binding of colchicine to tubulin. A computational analysis of the binding of HMBA to tubulin supported the finding that HMBA shared its binding site with colchicine in tubulin and indicated that the binding of HMBA to tubulin was primarily stabilized through hydrogen bonding.

On the Structure of the Proton-Binding Site in the Fo Rotor of Chloroplast ATP Synthases

The recently reported crystal structures of the membrane-embedded proton-dependent c-ring rotors of a cyanobacterial F1Fo ATP synthase and a chloroplast F1Fo ATP synthase have provided new insights into the mechanism of this essential enzyme. While the overall features of these c-rings are similar, a discrepancy in the structure and hydrogen-bonding interaction network of the H+ sites suggests two distinct binding modes, potentially reflecting a mechanistic differentiation. Importantly, the conformation of the key glutamate side chain to which the proton binds is also altered. To investigate the nature of these differences, we use molecular dynamics simulations of both c-rings embedded in a phospholipid membrane. We observe that the structure of the c15 ring from Spirulina platensis is unequivocally stable within the simulation time. By contrast, the proposed structure of the H+ site in the chloroplast c14 ring changes rapidly and consistently into that reported for the c15 ring, indicating that the latter represents a common binding mode. To assess this hypothesis, we have remodeled the c14 ring by molecular replacement using the published structure factors. The resulting structure provides clear evidence in support of a common binding site conformation and is also considerably improved statistically. These findings, taken together with a sequence analysis of c-subunits in the ATP synthase family, indicate that the so-called proton-locked conformation observed in the c15 ring may be a common characteristic not only of light-driven systems such as chloroplasts and cyanobacteria but also of a selection of other bacterial species.

Numerous Isomers of Serine Octamer Ions Characterized by Infrared Photodissociation Spectroscopy

Numerous Isomers of Serine Octamer Ions Characterized by Infrared Photodissociation Spectroscopy

Detection and trapping of intermediate states priming nicotinic receptor channel opening

In the course of synaptic transmission in the brain and periphery, acetylcholine receptors (AChRs) rapidly transduce a chemical signal into an electrical impulse. The speed of transduction owes in large part to rapid ACh association and dissociation, implying a binding site relatively non-selective for small cations; selective transduction has been supposed to originate from the ability of ACh, over that of other organic cations, to trigger the subsequent channel opening step. However transitions to and from the open state were shown to be similar for agonists with widely different efficacies.1,2,3 Here, by studying mutant AChRs, we find that the ultimate closed to open transition is agonist-independent and preceded by two primed closed states; the first primed state elicits brief openings, whereas the second elicits long-lived openings. Long-lived openings and the associated primed state are detected in the absence and presence of agonist, and exhibit the same kinetic signatures under both conditions. By covalently locking the agonist binding sites in the bound conformation, we find that each site initiates a priming step. Thus a change in binding site conformation primes the AChR for channel opening in a process that enables selective activation by ACh while maximizing speed and efficiency of the biological response.

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

The representation of protein flexibility is still a challenge for the state-of-the-art flexible ligand docking protocols. In this article, we use a large and diverse benchmark to prove that is possible to improve consistently the cross-docking performance against a single receptor conformation, using an equilibrium ensemble of binding site conformers. The benchmark contained 28 proteins, and our method predicted the top-ranked near native ligand poses 20% more efficiently than using a single receptor. The multiple conformations were derived from the collective variable space defined by all heavy-atom elastic network normal modes, including backbone and side chains. We have found that the binding site displacements for best positioning of the ligand seem rather independent from the global collective motions of the protein. We also found that the number of binding site conformations needed to represent nonredundant flexibility was < 100. The ensemble of receptor conformations can be generated at our Web site at http://abagyan.scripps.edu/MRC.

Gating Current Measurements Reveal Ligand-Selective Conformational Changes in the M2 Muscarinic Receptor

In addition to external stimuli, membrane voltage modulates the activity of several G-protein-coupled receptors (GPCRs). For example, membrane depolarization reduces the affinity of the M2 muscarinic receptor (M2R) for acetylcholine (ACh). The intrinsic capacity of muscarinic receptors to “sense” transmembrane potential was confirmed by the recording of “gating” currents that reflect reorientation of charges within the receptor in response to changes in voltage. We studied the effects of membrane voltage on agonist activation of M2R in atrial myocytes and on gating currents in oocytes heterologously expressing M2R. Depolarization decreased the apparent affinity of M2R for ACh, but increased the apparent affinity and efficacy of pilocarpine (PILO), as measured by acetylcholine-activated K+ current, IKACh. Voltage-induced conformational changes in M2R (as measured by gating currents) were modified in a ligand-selective manner. For example, ACh reduced gating charge displacement while PILO increased the amount of charge displaced. Thus, these ligands manifest opposite voltage-dependent IKACh modulation and exert opposite effects on M2R gating charge displacement. Finally, mutations in the putative ligand binding site perturbed the movement of the M2R voltage sensor and confirmed a link between voltage sensing and changes in agonist affinity. Our data suggest that voltage modulates the conformation of the ligand binding site, while ligand binding induces ligand-specific conformational changes in the receptor. Voltage-dependent GPCR modulation has important implications for cellular signaling in excitable tissues. Gating current measurement allows for the tracking of subtle conformational changes in the receptor that accompany ligand binding and changes in membrane voltage.

Detection and Trapping of Elusive Priming Intermediates Towards Open Nicotinic Receptor Channel

Acetylcholine receptors (AChRs) mediate rapid synaptic transmission by transducing a chemical signal into an electrical impulse. Transduction comprises binding of agonist followed by opening of the AChR ion channel, and in the classical view both processes depend on the agonist. However previous studies suggest the ultimate channel opening step is agonist-independent1,2, and is preceded by a priming step facilitated by the agonist3. Here, by studying mutant AChRs, we detect two such priming steps; the first generates a closed state that elicits brief openings, and the second generates a closed state that elicits long-lived openings. Long-lived openings and the associated priming step are detected in the absence of agonist and in its presence, and show identical kinetics under each condition. By covalently locking the agonist binding sites in the bound conformation, we show that each site initiates a priming step. Thus a change in binding site conformation primes the AChR for channel opening in a process that determines the maximum response to agonist and functional consequences of disease-causing mutations.

Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family

Methods for analyzing complete gene families are becoming of increasing importance to the drug discovery process, because similarities and differences within a family are often the key to understanding functional differences that can be exploited in drug design. We undertake a large-scale structural comparison of protein kinase ATP-binding sites using a geometric hashing method. Subsequently, we propose a relevant classification of the protein kinase family based on the structural similarity of its binding sites. Our classification is not only able to reveal the great diversity of different protein kinases and therefore their different potential for inhibitor selectivity but it is also able to distinguish subtle differences within binding site conformation reflecting the protein activation state. Furthermore, using experimental inhibition profiling, we demonstrate that our classification can be used to identify protein kinase binding sites that are known experimentally to bind the same drug, demonstrating that it has potential as an inverse (protein) virtual screening tool, by identifying which other sites have the potential to bind a given drug. In this way the cross-reactivities of the anticancer drugs Tarceva and Gleevec are rationalized.

Influence of neurophysin residues 1-8 on the optical activity of neurophysin-peptide complexes. Direct evidence that the 1-8 sequence alters the environment of bound peptide.

Circular dichroism was used to compare the environment of peptides bound to native and des 1-8 neurophysin in order to further elucidate the role of the neurophysin 1-8 sequence in peptide-binding. A very large positive ellipticity (approximately 6000 deg cm2 dmol-1), shown earlier to be induced in tyrosine at position 2 of peptides bound to the native protein, was determined by the present study to be paralleled by similar induced changes in tyrosine at peptide position 1. Deletion of the neurophysin 1-8 sequence led to loss of half of the induced optical activity at peptide positions 1 and 2 and changes in binding-induced optical activity in the protein, the latter partially assignable to protein disulfides. In the mononitrated native and des 1-8 proteins, the optical activity of neurophysin Tyr-49, a residue at the peptide-binding site, was reduced by 80% in complexes of the des 1-8 protein relative to those of the native protein. The results suggest a role for neurophysin Arg-8 in modulating the optical activity at the binding site by directly placing a charge proximal to the binding site and/or by altering binding site conformation. The data provide the first unambiguous evidence of a difference in the environment of bound peptide between the native and des 1-8 proteins.

P03-210 Conformation of albumin binding sites are disturbed in schizophrenia

Aim:Investigate some properties of albumin binding sites in schizophrenic patients.Methods:Properties of serum albumin binding sites were studied using quenching of fluorescence of probe K-35 (N-carboxyphenylimide of dimethylaminonaphthalic acid) with nitrate anion. Serum samples were collected from 24 schizophrenic patients and 24 healthy volunteers.Results:In the absence of quencher specific probe fluorescence in patients was 1,4 times higher than in controls. Fluorescent quenching constant for probe bound to albumin was 2,5 L/mol in patients versus 4,6 L/mol in volunteers (p&lt; 0,01). Fluorescent fraction assessable to quenching was significantly lower in patients than in volunteers. Fluorescent decay studies on S-60 synchrotron have revealed in patient's albumin the redistribution between long-lived and short-lived molecules of the probe with increase of the latter. There were found decrease of albumin accessible SH-groups in schizophrenic patients as compared with volunteers.Conclusions:In schizophrenic patients conformational state of albumin binding sites is significantly disturbed that can lead to changes in protein-ligand interaction and to damage of main albumin functions (transport and detoxification) and aggravation of endotoxicosis.

Structural model and functional significance of pH-dependent talin–actin binding for focal adhesion remodeling

Actin filament binding by the focal adhesion (FA)-associated protein talin stabilizes cell-substrate adhesions and is thought to be rate-limiting in cell migration. Although F-actin binding by talin is known to be pH-sensitive in vitro, with lower affinity at higher pH, the functional significance of this pH dependence is unknown. Because increased intracellular pH (pH(i)) promotes cell migration and is a hallmark of metastatic carcinomas, we asked whether it increases FA remodeling through lower-affinity talin-actin binding. Talin contains several actin binding sites, but we found that only the COOH-terminal USH-I/LWEQ module showed pH-dependent actin binding, with lower affinity and decreased maximal binding at higher pH. Molecular dynamics simulations and NMR of this module revealed a structural mechanism for pH-dependent actin binding. A cluster of titratable amino acids with upshifted pK(a) values, including His-2418, was identified at one end of the five-helix bundle distal from the actin binding site. Protonation of His-2418 induces changes in the conformation and dynamics of the remote actin binding site. Structural analyses of a mutant talin-H2418F at pH 6.0 and 8.0 suggested changes different from the WT protein, and we confirmed that actin binding by talin-H2418F was relatively pH-insensitive. In motile fibroblasts, increasing pH(i) decreased FA lifetime and increased the migratory rate. However, expression of talin-H2418F increased lifetime 2-fold and decreased the migratory rate. These data identify a molecular mechanism for pH-sensitive actin binding by talin and suggest that FA turnover is pH-dependent and in part mediated by pH-dependent affinity of talin for binding actin.

Role of residues in the adenosine binding site of NAD of the Ascaris suum malic enzyme

Ascaris suum mitochondrial malic enzyme catalyzes the divalent metal ion dependent conversion of l-malate to pyruvate and CO 2, with concomitant reduction of NAD(P) to NAD(P)H. In this study, some of the residues that form the adenosine binding site of NAD were mutated to determine their role in binding of the cofactor and/or catalysis. D361, which is completely conserved among species, is located in the dinucleotide-binding Rossmann fold and makes a salt bridge with R370, which is also highly conserved. D361 was mutated to E, A and N. R370 was mutated to K and A. D361E and A mutant enzymes were inactive, likely a result of the increase in the volume in the case of the D361E mutant enzyme that caused clashes with the surrounding residues, and loss of the ionic interaction between D361 and R370, for D361A. Although the K m for the substrates and isotope effect values did not show significant changes for the D361N mutant enzyme, V/ E t decreased by 1400-fold. Data suggested the nonproductive binding of the cofactor, giving a low fraction of active enzyme. The R370K mutant enzyme did not show any significant changes in the kinetic parameters, while the R370A mutant enzyme gave a slight change in V/ E t, contrary to expectations. Overall, results suggest that the salt bridge between D361 and R370 is important for maintaining the productive conformation of the NAD binding site. Mutation of residues involved leads to nonproductive binding of NAD. The interaction stabilizes one of the Rossmann fold loops that NAD binds. Mutation of H377 to lysine, which is conserved in NADP-specific malic enzymes and proposed to be a cofactor specificity determinant, did not cause a shift in cofactor specificity of the Ascaris malic enzyme from NAD to NADP. However, it is confirmed that this residue is an important second layer residue that affects the packing of the first layer residues that directly interact with the cofactor.