Cytochrome P450 active site plasticity: attenuation of imidazole binding in cytochrome P450(cam) by an L244A mutation

We have identified a P450(cam) mutation, L244A, that mitigates the affinity for imidazole and substituted imidazoles while maintaining a high affinity for the natural substrate camphor. The P450(cam) L244A crystal structure solved in the absence of any ligand reveals that the I-helix is displaced inwards by over 1 A in response to the cavity created by the change from leucine to alanine. Furthermore, the crystal structures of imidazole-bound P450(cam) and the 1-methylimidazole-bound P450(cam) L244A mutant reveal that the ligands have distinct binding modes in the two proteins. Whereas in wild-type P450(cam) the imidazole coordinates to the iron in an orientation roughly perpendicular to the plane of the heme, in the L244A mutant the rearranged I helix, and specifically residue Val247, forces the imidazole into an orientation almost parallel to the heme that impairs its ability to coordinate to the heme iron. As a result, the imidazole is much more weakly bound to the mutant than it is to the wild-type enzyme. Despite the constriction of the active site by the mutation, previous work with the L244A mutant has shown that it oxidizes larger substrates than the wild-type enzyme. This paradoxical situation, in which a mutation that nominally increases the active site cavity appears to decrease it, suggests that the mutation actually increases the active site maleability, allowing it to better expand to oxidize larger substrates.     

Structure-activity correlations in pentachlorobenzene oxidation by engineered cytochrome P450cam

We had reported engineering of the heme monooxygenase cytochrome P450cam from Pseudomonas putida with the F87W/Y96F/L244A/V247L mutations for the oxidation of pentachlorobenzene (PeCB), a recalcitrant environmental contaminant, to pentachlorophenol. In order to provide further insights into P450 structure, function and substrate recognition, we have determined the crystal structure of this 4-mutant without a substrate and its complex with PeCB. PeCB is bound face-on to the heme, with a weak Fe--Cl interaction. One PeCB chlorine is located in the cavity generated by the L244A mutation, in striking illustration of the role of this mutation in promoting PeCB binding. The structures also show that the P450(cam) oxygen-binding groove between G248 and T252 is flexible and can tolerate significant deviations from their conformations in the wild type without loss of enzyme activity. Analysis of the PeCB binding interactions led to introduction of the T101A mutation to enable the substrate to reorient during the catalytic cycle for more efficient oxidation. The resultant 5-mutant F87W/Y96F/T101A/L244A/V247L is 3-fold more active for PeCB oxidation than the 4-mutant. Polychlorinated benzene binding by the mutants and the partitioning between substrate oxidation and non-productive (uncoupling) side reactions are correlated with the structural data.     

Intramolecular electron transfer in a cytochrome P450cam system with a site-specific branched structure

Cytochrome P450 (P450) is an attractive oxygenase due to the diverse catalytic reactions and the broad substrate specificity. Class I P450s require an excess concentration (more than 10 times) of iron-sulfur proteins, which transfer electrons to P450s, to attain the maximum catalytic activity and this requirement is a critical bottleneck for practical applications. Here, we show a site-specific branched fusion protein of P450 with its electron transfer proteins using enzymatic cross-linking with transglutaminase. A branched fusion protein of P450 from Pseudomonas putida (P450cam), which was composed of one molecule each of P450cam, putidaredoxin (Pdx) and Pdx reductase, showed higher catalytic activity (306 min(-1)) and coupling efficiency (99%) than the equimolar reconstitution system due to the intramolecular electron transfer. The unique site-specific branched structure simply increased local concentration of proteins without denaturation of each protein. Therefore, enzymatic post-translational protein manipulation can be a powerful alternative to conventional strategies for the creation of multicomponent enzyme systems with novel proteinaceous architecture.     

Comparison of the construction of a 3-D model for human thromboxane synthase using P450cam and BM-3 as templates: implications for the substrate binding pocket

A 3-D model of human thromboxane A₂ synthase (TXAS) was constructedusing a homology modeling approach based on information fromthe 2.0 crystal structure of the hemoprotein domains of cytochromeP450BM-3 and P450cam. P450BM-3 is a bacterial fatty acid monooxygenaseresembling eukaryotic microsomal cytochrome P450s in primarystructure and function. TXAS shares 26.4% residue identity and48.4% residue similarity with the P450BM-3 hemoprotein domain.The homology score between TXAS and P450BM-3 is much higherthan that between TXAS and P450cam. Alignment between TXAS andthe P450BM-3 hemoprotein domain or P450cam was determined throughsequence searches. The P450BM-3 or P450cam main-chain coordinateswere spplied to the TXAS main chain in those sements where thetwo sequences were well aligned. These segments were linkedto one another using a fragment search method, and the sidechains were added to produce a 3-D model for TXAS. A TXAS substrate,prostaglandin H₂ (PGH₂) was docked into the TXAS cavity correspondingto the arachidonic acid binding pocket in P450BM-3 or camphorbinding site in P450cam. Regions of the heme and putative PGH2binding cavities in the TXAS model were identified and analyzed.The segments and residues involved in the active-site pocketof the TXAS model provide reasonable candidates for TXAS proteinengineering and inhibitor design. Comparison of the TXAS modelbased on P450BM-3 with another TXAS model based on the P450BM-3with another TXAS model based on the P450cam structure indicatedthat P450BM-3 is a more suitable template for homology modelingof TXAS.     

Construction and evaluation of a three-dimensional structure of cytochrome P450choP enzyme (CYP105C1)

The purpose of this work was to develop and carefully evaluateimproved strategies for constructing reliable 3-D models ofP450 isozymes. To this end, a unique combination of steps forbuilding and evaluating a model structure was used to builda homology model of the P450choP isozyme, based on knowledgeof the X-ray structures of P450cam, P450terp, P450BM-3 and P450eryF.Specifically, the reliability of this model was examined bysystematic comparisons of its conformational, energetic, environmentaland packing properties and those of the four reference proteinswith corresponding properties from the database of proteinswith known structures. The results showed that the examinedproperties of this model structure are well within the criteriaestablished for reliable structures and are of nearly as goodquality as those of the reference proteins. In addition, theresult from a 120 ps unconstrained MD simulation of the modelwith structural waters provided evidence that the model is stableat room temperature. This 3-D model can now be reliably usedfor explicit characterization of substrate and inhibitor complexes.Most importantly, although it is envisioned that building modelsfor mammalian P450s will be even more challenging, the stepsdescribed here should be very useful in future constructionof 3-D models of mammalian P450 isozymes.     

Sequence requirements for cytochromes P450IIA1 and P450IIA2 catalytic activity: evidence for both specific and non-specific substrate binding interactions through use of chimeric cDNAs and cDNA expression

Cytochrome P450s IIA1 and IIA2, encoded by the CYP2A1 and CYP2A2genes, display 88% amino acid sequence similarities. The dissimilaritiesof sequence between these two enzymes are primarily localizedwithin four discrete regions of the polypeptides that are separatedby regions of absolute sequence identity. IIA1 specificallyhydroxylates the prototype substrate testosterone at the 7 and6 position with a predominance of 7 metabolite. IIA2, on theother hand, hydroxylates this steroid at eight positions onthe molecule, with one of the most abundant metabolites being15hydroxytestosterone. To determine those amino acids responsiblefor the difference in testosterone hydroxylation specificities,chimeras were constructed between IIA1 and IIA2 cDNAs and expressedin cell culture using vaccinia-virus-mediated cDNA expression.Chimeras, in which the first 355 amino acids correspond to asingle enzyme, maintain the specificity associated with thatenzyme. Of six chimeras which have substitutions between aminoacids 161 and 276, two are inactive and the remaining four givesimilar metabolite profiles, in which both 7 and 15 hydroxylationspecificities have been lost. Two of these four chimeras arediametric apposites, suggesting that modification of eitherthe N-terminal or central regions of the enzymes results inconformational changes that prevent the specific binding interactionsresponsible for the narrow regioselectivity associated withIIA1 and 15-hydroxytestosterone formation associated with IIA2.     

Prediction of the three-dimensional structure of human interleukin-7 by homology modeling

The three-dimensional structure of human interleukin (IL)-7has been predicted based on homology to human IL-2, IL-4, granulocyte-macrophagecolony stimulating factor and growth hormone. The model hasa topology common to other cytokines anddisplays a unique disulfidepattern. Knowledge of the tertiary structure of IL-7 has implicationsfor analysis of key binding regions, suggestions for mutagenesisexperiments and design of (ant)agonists. In this context, themodel is discussed and compared with other cytokine structures.     

Ile115Leu mutation in the SRS1 region of an insect cytochrome P450 (CYP6B1) compromises substrate turnover via changes in a predicted product release channel

CYP6B1 represents the principal cytochrome P450 monooxygenase responsible for metabolizing furanocoumarins in Papilio polyxenes, an insect that specializes on host plants containing these toxins. Investigations of the amino acids responsible for the efficient metabolism of these plant toxins has identified Ile115 as one that modulates the rate of furanocoumarin metabolism even though it is predicted to be positioned at the edge of the heme plane and outside substrate contact regions. In contrast to previous expression studies conducted under conditions of limiting P450 reductase showing that the Ile115-to-Leu replacement enhances turnover of xanthotoxin and other furanocoumarins, studies conducted at high P450 reductase indicate that the Ile115-to-Leu replacement reduces turnover of these substrates. Further analysis of substrate binding affinities, heme spin state and NADPH consumption rates indicate that, whereas the I115L replacement mutant displays higher substrate affinity and heme spin state than the wild-type CYP6B1 protein, it utilizes NADPH more slowly than the wild-type CYP6B1 protein at high P450 reductase levels. Molecular models developed for the wild-type CYP6B1 and mutant protein suggest that more constricted channels extending from the catalytic site in the I115L mutant to the P450 surface limit the rate of product release from this mutant catalytic site under conditions not limited by the rate of electron transfer from NADPH.     

Binding free energy calculations for P450cam-substrate complexes

A recently proposed semi-empirical method for calculating bindingfree energies was used to examine the binding of a variety ofsubstrates to cytochrome P450cam. For a set of 11 differentpotential substrates of cytochrome P450cam, both the absoluteand relative binding free energies were generally well reproduced.The mean error in the calculated absolute binding free energyfor all 11 compounds is 0.55 kcal/mol. Forty-eight out of 55calculated relative binding free energies have the correct signand the mean unsigned error between calculated and experimentalrelative binding free energies is 0.77 kcal/mol. For one substrate,thiocamphor, the effect of substrate orientation on the calculatedbinding free energy was examined. The ability of this methodto predict the effect of active site mutations was also examinedin two cases.     

Class-dependent sequence alignment strategy improves the structural and functional modeling of P450s

Different procedures for obtaining homology models for P450s are investigated using various sequence alignments sharing various levels of sequence identity with available P450 crystal structures. In this analysis, we have investigated how well homology modeling can reproduce known crystal structures as well as how effectively these homology models can be used to reproduce known ligand-binding modes. Homology models obtained from sequence alignments that discriminate between Class I and Class II P450s are significantly closer to the experimental crystal structures and more closely reproduce known ligand's binding modes, than those obtained using sequence alignments that combine Class I and Class II P450s. The quality of the models is slightly improved by constructing hybrid-structure models that model three of the most variable regions of P450s independently from the rest of the protein: the B region that includes SRS1, the FG region that includes SRS2 and SRS3 and the beta4 region that includes SRS6.     

Three-dimensional structure of protein C inhibitor predicted from structure of {alpha}1-antitrypsin with computer graphics

The three-dimensional structure of a proteolytically modifiedprotein C inhibitor, a member of the serine protease inhibitorsuperfamily, was constructed with computer graphics based onits amino acid sequence homology with that of the modified 1-antitrypsinwhose structure had been elucidated by X-ray crystallography.The intact form of protein C inhibitor was predicted with an-carbon model based on its hydrophilicity and hydrogen bondpattern. Furthermore, a model of its interaction with activatedprotein C was constructed based on the structure of the complexbetween trypsin and its inhibitor, which had been determinedby X-ray crystallography.     

A predicted three-dimensional structure for the human immunodeficiency virus binding domains of CD4 antigen

A predicted three-dimensional structure of the two N-terminalextracellular domains of human CD4 antigen, a cell surface glycoprotein,is reported. This region of CD4, particularly the first domain,has been identified as containing the binding region for theenvelope gp120 protein of the human immuno-deficiency virus.The model was predicted based on the sequence homology of eachdomain with the variable light chain of immunoglobulins. Theframework ß-sheet regions were taken from the crystalcoordinates of REI. For one region in the first domain of CD4there was an ambiguity in the alignment with REI and two alternatemodels are presented. Loops connecting the framework were modeledfrom fragments selected from a database of main chain coordinatesfrom all known protein structures. Residues identified as involvedin binding gp120 have been located in several other studieswithin the first domain of CD4. Epitopes from eight monoclonalantibodies have been mapped onto residues in both domains. Competitionof these antibodies with each other and with gp120 can be interpretedfrom the structural model.     

Engineering mammalian cytochrome P450 2B1 by directed evolution for enhanced catalytic tolerance to temperature and dimethyl sulfoxide

The previously laboratory-evolved cytochrome P450 2B1 quadruple mutant V183L/F202L/L209A/S334P (QM), which showed enhanced H(2)O(2)-mediated substrate oxidation, has now been shown to exhibit a >3.0-fold decrease in K(m,HOOH) for 7-ethoxy-4-trifluoromethylcoumarin (7-EFC) O-deethylation compared with the parental enzyme L209A. Subsequently, a streamlined random mutagenesis and a high-throughput screening method were developed using QM to screen and select mutants with enhanced tolerance of catalytic activity to temperature and dimethyl sulfoxide (DMSO). Upon screening >3000 colonies, we identified QM/L295H and QM/K236I/D257N with enhanced catalytic tolerance to temperature and DMSO. QM/L295H exhibited higher activity than QM at a broad range of temperatures (35-55 degrees C) and maintained approximately 1.4-fold higher activity than QM at 45 degrees C for 6 h. In addition, QM/L295H showed a significant increase in T(m,app) compared with L209A. QM/L295H and QM/K236I/D257N exhibited higher activity than QM at a broad range of DMSO concentrations (2.5-15%). Furthermore, QM/K236I/D257N/L295H was constructed by combining QM/K236I/D257N with L295H using site-directed mutagenesis and exhibited a >2-fold higher activity than QM at nearly the entire range of DMSO concentrations. In conclusion, in addition to engineering mammalian cytochromes P450 for enhanced activity, directed evolution can also be used to optimize catalytic tolerance to temperature and organic solvent.     

Engineering cytochrome P-450cam to increase the stereospecificity and coupling of aliphatic hydroxylation

Site-directed mutants were constructed in cytochrome P-450_camto re-engineer the stereochemistry and coupling of ethylbenzenehydroxyiation. The reaction with wild-type (WT) enzyme producesone regioisomer 1-phenylethanol with 5% reduced nicotinamideadenine deoxyribonucleic acid to product conversion of and aratio of 73:27 for the R and S enantiomers respectively. Ethyibenzenewas modeled into the active site of WT P-450_cam in a rigid modeand oriented to optimize either pro-R or pro-S hydrogen abstraction.Residues T101, T185 and V247 make extensive contacts with thesubstrate in the static complexes and were therefore chosenfor site-directed mutagenesis. Single mutants T101M, V247A andV247M are more stereospedik producing 89,87 and 82% (R)-1-phenylethanolrespectively. The coupling of the reaction is doubled for thesingle mutants T185L, T185F and V247M. In an effort to engineerincreased stereospecificity and coupling into a single catalystthe T101M, T185F and V247M mutants were combined in a multiplemutant of P-450_cam.This protein hydroxylates ethyibenzene resultingin an R:S ratio of 87:13 for the 1-phenylethanols and 13% couplingof reducing equivalents to product. The catalytic stereospecificityand stoichiometry with T101M–T185F–V247M does notrepresent a summation of the changes observed for the singlemutants. A portion of the individual effects on substrate recognitionproduced by the single substitutions is either eliminated ordegenerate within the triple mutant.     

Enzyme-catalyzed dehalogenation of pentachloroethane: why F87W-cytochrome P450cam is faster than wild type

Under anaerobic conditions, cytochromes P450 can reductivelydehalogenate heavily halogenated hydrocarbons, such as one-and two-carbon organic solvents. This catalytic capacity hasdrawn attention to the potential use of engineered forms ofP450s in the remediation of contaminated deep subsurface ecosystems.Loida (1994, PhD Thesis, University of Illinois at Urbana-Champaign,IL) and S.G.Sligar (personal communication) have observedrecentlythat an active-site variant of cytochrome P450cam (F87W) dechlorinatespentachloroethane approximately three times faster than thewild-type enzyme. Molecular dynamics simulations have revealedthat the mutant enzyme binding pocket remains smaller, and thatpentachloroethane assumes configurations closer to the heme-Fein the F87W mutant twice as often as in the wild-type enzyme.This result is consistent with a collisional model of dehalogenation,which agrees with experimental observations [Li and Wackett(1993) Biochemistry, 32, 9355–9361] that solutions containingwild-type P450cam dehalogenate pentachloroethane 100 times fasterthan those containing free heme. The simulations suggest thatit is unlikely that Trp87 significantly stabilizes the developingnegative charge on the substrate during carbon-halogen bondreduction. The design of improved microbiai enzymes that incorporateboth steric and electronic effects continues for use in remediatinghalogenated contaminants in situ     

Prediction and analysis of SH2 domain-phosphopeptide interactions

Src homology 2 (SH2) domains are small protein modules of -100amino acids that are found in many proteins involved in intracellularsignal transduction. They mediate protein-protein interactionsand modulate enzyme activity by their ability to bind to specificsequence patterns that contain a phosphorylated tyrosine. Asthe three-dimensional structures of the phosphatidylinositol(PI) 3-kinase, Lck, Src and Abl SH2 domains have been shownto be similar, we have modelled other SH2 domains that showdistinct sequence specificity to allow comparative analysisof SH2-phosphopeptide interactions. The SH2 domains of PLC-Nterm.,Nck, Grb2, GAP and Abl have been model-built with high-affinityphosphopeptides fitted into the putative binding sites. Foreach SH2 domain a detailed analysis of the peptide-protein interactionwas performed. It is apparent that specificity is mainly conferredby three to five residues downstream from the phosphotyrosineresidue (Y*), especially, although not exclusively, peptideposition Y* + 3. The SH2 pocket that binds the Y* + 3 residueis mainly composed of three sections: part of strand (ßEgoing into loop EF, part of B and loop BG. The residues thatconstitute the Y* +3 binding pocket show variability that seemsto determine which amino acid binds preferentially. Residueposition ßE4 seems to play a vital role in the SH2specificity. This study shows that the development of modellingprotocols for SH2 domains whose structure has not been determinedcan prove very useful in predicting which residues are involvedin conferring the affinity and binding specificity of thesedomains towards distinct phosphotyrosine-containing sequences.     

Model building of disulfide bonds in proteins with known three-dimensional structure

As an aid in the selection of sites in a protein where a disulfidebond might be engineered, a computer program has been developed.The algorithm starts with the generation of Cß positionsfrom the N, C and C atom coordinates available from a three-dimensionalmodel. A first set of residue pairs that might form a disulfidebond is selected on the basis of Cß–Cßdistances between residues. Then, for each residue in this set,S positions are generated, which satisfy the requirement that,with ideal values for the C–Cß and Cß–Sbond lengths and for the bond angle at Cß, the distancebetween S of residue 1 and Cß of residue 2 in a pair(determined by the bond angle at S2) is at, or very close toits ideal value. Usually two acceptable S positions are foundfor each half cystine, resulting in up to four different conformationsfor the disulfide bond. Finally, these conformations are subjectedto an energy minimization procedure to remove large deviationsfrom ideal geometry and their final energies are calculated.User input determines which final conformations are energeticallyacceptable. These conformations are written to a file to allowfurther analysis and e.g. inspection on a computer graphicsdevice.     

What function for human lithostathine?: structural investigations by three-dimensional structure modeling and high-resolution NMR spectroscopy

Human lithostathine is a 144-residue protein, expressed in variousorgans and pathologies. Several biological functions have beenproposed for this protein. Among others, inhibition of nucleationand growth of CaCO₃ crystals in the pancreas and bacterial aggregationhas retained attention, because lithostathine presents highsequence similarities with calcium-dependent (or C-type) lectins.To study its structure-function relationship and compare itwith that of C-type lectins, we have built a model for lithostathine.This model is derived from the only two C-type lectins of knownstructures: rat mannose binding protein and human E-selectin.An original strategy, inspired by that proposed by Havel andSnow, was designed for model building. We have undertaken NMRstudies on the natural protein. Although complete structuredetermination has not yet been achieved, the NMR studies didconfirm the main characteristics of the model. From analysisof the proposed model, we concluded that lithostathine is notexpected to present sugar- or calcium-binding properties. Therefore,the mechanisms of bacterial aggregation and inhibition of CaCO₃nucleation and growth have not yet been elucidated.     

Homology modeling study of the human interleukin-7 receptor complex

Following a recent model of human interleukin-7 (IL-7), we presenthere a modeling study of the extracellular part of the humanIL-7 receptor complex, including the IL-7 specific (IL-7R) andthe common gamma (_c) chains. The investigation is based on structuralhomology to the complex of human growth hormone (hGH) boundto its receptor (hGHR). For domain 1 of IL-7R two differentmodels are presented which differ in the alignment to hGHR inthree regions. However, these differences affect binding toIL-7 in only one region, at the interface between loop EF ofdomain 1 of IL-7R and helix C of IL-7. The disulfide patternin domain 1 of IL-7R is predicted to deviate from that observedin hGHR in that the C'–E disulfide (hGHR) is replacedby a C-C' cross-link. The prediction for the _c chain is comparedwith two previous studies. The models of the complex provideinsight into the binding of IL-7 to its receptor and have implicationsfor the suggestion of mutagenesis experiments and the designof (ant)agonists.     

Cytochrome P450 Enzymes and Drug Metabolism in Humans

Human cytochrome P450 (CYP) enzymes, as membrane-bound hemoproteins, play important roles in the detoxification of drugs, cellular metabolism, and homeostasis. In humans, almost 80% of oxidative metabolism and approximately 50% of the overall elimination of common clinical drugs can be attributed to one or more of the various CYPs, from the CYP families 1–3. In addition to the basic metabolic effects for elimination, CYPs are also capable of affecting drug responses by influencing drug action, safety, bioavailability, and drug resistance through metabolism, in both metabolic organs and local sites of action. Structures of CYPs have recently provided new insights into both understanding the mechanisms of drug metabolism and exploiting CYPs as drug targets. Genetic polymorphisms and epigenetic changes in CYP genes and environmental factors may be responsible for interethnic and interindividual variations in the therapeutic efficacy of drugs. In this review, we summarize and highlight the structural knowledge about CYPs and the major CYPs in drug metabolism. Additionally, genetic and epigenetic factors, as well as several intrinsic and extrinsic factors that contribute to interindividual variation in drug response are also reviewed, to reveal the multifarious and important roles of CYP-mediated metabolism and elimination in drug therapy.