The xenobiotic metabolizing cytochromes P450 (P450s) are among the most versatile biological catalysts known, but knowledge of the structural basis for their broad substrate specificity has been limited. P450 2B4 has been frequently used as an experimental model for biochemical and biophysical studies of these membrane proteins. A 1.6-Å crystal structure of P450 2B4 reveals a large open cleft that extends from the protein surface directly to the heme iron between the ␣-helical and ␤-sheet domains without perturbing the overall P450 fold. This cleft is primarily formed by helices B to C and F to G. The conformation of these regions is dramatically different from that of the other structurally defined mammalian P450, 2C5/3LVdH, in which the F to G and B to C regions encapsulate one side of the active site to produce a closed form of the enzyme. The open conformation of 2B4 is trapped by reversible formation of a homodimer in which the residues between helices F and G of one molecule partially fill the open cleft of a symmetryrelated molecule, and an intermolecular coordinate bond occurs between H226 and the heme iron. This dimer is observed both in solution and in the crystal. Differences between the structures of 2C5 and 2B4 suggest that defined regions of xenobiotic metabolizing P450s may adopt a substantial range of energetically accessible conformations without perturbing the overall fold. This conformational flexibility is likely to facilitate substrate access, metabolic versatility, and product egress. T he cytochromes P450 (P450s) are a superfamily of hemecontaining monooxygenases. They are responsible for the metabolism of an unusually wide range of endogenous and exogenous substrates, including synthesis of steroid hormones, bile acids, and cholesterol, and the degradation of steroids, fatty acids, drugs, toxins, and procarcinogens (1). P450s from families 1, 2, and 3 have evolved to convert lipophilic xenobiotics to more polar metabolites readily conjugated by phase II enzymes, and thus targeted for elimination. The stereo-and regiospecificity of metabolite formation by individual xenobiotic metabolizing P450s suggest very specific substrate-enzyme interactions, whereas the range of substrates metabolized suggests an induced fit type of substrate recognition. Understanding the basis for this specific, yet versatile, metabolism by mammalian xenobiotic metabolizing P450s has been limited by the dearth of structural information for these membrane proteins.In 2000, the first mammalian P450 structure was published (2, 3), that of P450 2C5, which was engineered to delete the single N-terminal transmembrane domain and to mutate a peripheral membrane-binding site. Recent structures of 2C5 bound with the substrates, diclofenac (4) and 4-methyl-N-methyl-N-(2-phenyl-2H-pyrazol-3-yl)benzenesulfonamide (DMZ) (5), indicate that flexible regions of the protein adapt for substrate binding, and that ligands may bind in multiple orientations. The 2C5 structures generally reveal the enzyme closed around these substrates wi...

Chemokines play a fundamental role in trafficking of immune cells and in host defense against infection. The role of chemokines in the recruitment process is highly regulated spatially and temporally and involves interactions with G protein-coupled receptors and cell surface glycosaminoglycans. The dynamic equilibrium between chemokine monomers and dimers, both free in solution and in cell surface-bound forms, regulates different components of recruitment such as chemotaxis and receptor signaling. The binding and activity of the chemokine interleukin-8 (IL-8) for its receptors, previously studied using "trapped" non-associating monomers and non-dissociating dimers, show that the monomer has a native-like function but support conflicting roles for the dimer. We have measured the binding of native IL-8 to the CXCR1 N-domain, using isothermal titration calorimetry and sedimentation equilibrium techniques. The N-domain constitutes a critical binding site, and IL-8 binding affinity to the receptor N-domain is in the same concentration range as the IL-8 monomerdimer equilibrium. We observed that only the IL-8 monomer, and not the dimer, is competent in binding the receptor N-domain. Based on our results, we propose that IL-8 dimerization functions as a negative regulator for the receptor function and as a positive regulator for binding to glycosaminoglycans and that both play a role in the neutrophil recruitment process.

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We investigated the dynamics of isomerization and multi-channel dissociation of propenal (CH(2)CHCHO), methyl ketene (CH(3)CHCO), hydroxyl propadiene (CH(2)CH(2)CHOH), and hydroxyl cyclopropene (cyclic-C(3)H(3)-OH) in the ground potential-energy surface using quantum-chemical calculations. Optimized structures and vibrational frequencies of molecular species were computed with method B3LYP∕6-311G(d,p). Total energies of molecules at optimized structures were computed at the CCSD(T)∕6-311+G(3df,2p) level of theory. We established the potential-energy surface for decomposition to CH(2)CHCO + H, CH(2)CH + HCO, CH(2)CH(2)∕CH(3)CH + CO, CHCH∕CH(2)C + H(2)CO, CHCCHO∕CH(2)CCO + H(2), CHCH + CO + H(2), CH(3) + HCCO, CH(2)CCH + OH, and CH(2)CC∕cyclic-C(3)H(2) + H(2)O. Microcanonical rate coefficients of various reactions of trans-propenal with internal energies 148 and 182 kcal mol(-1) were calculated using Rice-Ramsperger-Kassel-Marcus and Variational transition state theories. Product branching ratios were derivable using numerical integration of kinetic master equations and the steady-state approximation. The concerted three-body dissociation of trans-propenal to fragments C(2)H(2) + CO + H(2) is the prevailing channel in present calculations. In contrast, C(3)H(3)O + H, C(2)H(3) + HCO and C(2)H(4) + CO were identified as major channels in the photolysis of trans-propenal. The discrepancy between calculations and experiments in product branching ratios indicates that the three major photodissociation channels occur mainly on an excited potential-energy surface whereas the other channels occur mainly on the ground potential-energy surface. This work provides profound insight in the mechanisms of isomerization and multichannel dissociation of the system C(3)H(4)O.

Escherichia coli cyclic AMP receptor protein (CRP) is a global transcriptional regulator which controls the expression of many different genes. Although different cyclic nucleotides can bind to CRP with almost equal affinity, only in the presence of cAMP could wild-type CRP bind to specific DNA sequences. Molecular genetic studies have identified a class of mutants, CRP*, which either do not require exogenous cAMP for activation or can be activated by cGMP. Thus, these mutants might aid in identifying the structural elements that are involved in the modulation of CRP to correctly differentiate the messages embedded in cyclic nucleotides. In this in vitro study, five CRP* mutants, namely, D53H, S62F, G141Q, G141K, and L148R, were tested for their abilities to bind the lac promoter sequence and the effects of cyclic nucleotides in modulating DNA sequence recognition. For comparison, non-CRP* mutants K52N, T127L, H159L, and K52N/H159L were studied. cCMP and cGMP can replace cAMP as an allosteric effector in all of these CRP mutants except S62F and non-CRP* mutants. The D53H, G141Q, G141K, and L148R mutants exhibit significantly higher affinity for the lac promoter sequence than wild-type CRP while S62F and the non-CRP* mutants exhibit reduced affinity. To probe the pathway of communication, the energetics of subunit assembly in these mutants were monitored by sedimentation equilibrium, and the conformational states of these mutants were probed by proteolysis and accessibility of Cys178 to chemical modifications. Results from these studies imply that signals due to mutations are mostly transmitted through the subunit interface. Thus, residues in CRP outside of the cyclic nucleotide binding site modulate the ability of CRP to differentiate these three cyclic nucleotides through long-range communication. Furthermore, this study shows that CRP* mutations do not impart any unique properties to CRP except that the DNA binding constants are shifted to a regime of higher affinity.

The ReacNetGenerator program can automatically extract reaction information from the reactive MD trajectory and construct reaction networks.

The contribution of conformational heterogeneity to cooperativity in cytochrome P450 3A4 was investigated using the mutant L211F/D214E/F304W. Initial spectral studies revealed a loss of cooperativity of the 1-pyrenebutanol (1-PB) induced spin shift (S 50 = 5.4 μM, n = 1.0) but retained cooperativity of α-naphthoflavone binding. Continuous variation (Job's titration) experiments showed the existence of two pools of enzyme with different 1-PB binding characteristics. Monitoring of 1-PB binding by fluorescence resonance energy transfer from the substrate to the heme confirmed that the high affinity site (K D = 0.3 μM) is retained in at least some fraction of the enzyme, although cooperativity is masked. Removal of apoprotein on a second column increased the high spin content and restored cooperativity of 1-PB binding and of progesterone and testosterone 6β-hydroxylation. The loss of cooperativity in the mutant is, therefore, mediated by the interaction of holo-and apo-P450 in mixed oligomers.

Repetitive DNA sequences are ubiquitous in life, and changes in the number of repeats often have various physiological and pathological implications. DNA repeats are capable of interchanging between different noncanonical and canonical conformations in a dynamic fashion, causing configurational slippage that often leads to repeat expansion associated with neurological diseases. In this report, we used single-molecule spectroscopy together with biophysical analyses to demonstrate the parity-dependent hairpin structural polymorphism of TGGAA repeat DNA. We found that the DNA adopted two configurations depending on the repeat number parity (even or odd). Transitions between these two configurations were also observed for longer repeats. In addition, the ability to modulate this transition was found to be enhanced by divalent ions. Based on the atomic structure, we propose a local seeding model where the kinked GGA motifs in the stem region of TGGAA repeat DNA act as hot spots to facilitate the transition between the two configurations, which may give rise to disease-associated repeat expansion.DNA tandem repeats | DNA slippage | single-molecule spectroscopy | X-ray crystallography D NA replication is a crucial process in all living organisms. Mishaps in the replication process generally lead to deleterious consequences but also drive biological evolution (1). Changes in the number of tandem copies of a specific DNA sequence within the genome are associated with devastating neuropathies and various types of cancer (2, 3). On the other hand, these changes also help shape normal genomic features such as microsatellite polymorphism, which are often used as markers for population biology studies (4).The unit sizes of repetitive DNA sequences involved in repeat number changes range from a single base (e.g., microsatellites) to dodecanucleotides (12 bases, e.g., in progressive myoclonic epilepsy type 1) (5, 6). DNA slippage is believed to be a primary mechanism driving the change in repeat number of various unit sizes. Repetitive DNA sequences often form alternative structures such as bulges and hairpin loops in addition to canonical DNA conformations (7,8). A repeat unit may slip between being part of a hairpin loop, a bulge, or a duplex in a dynamic fashion, which may alter the course of normal cellular DNA chemistry and ultimately lead to repeat expansion associated with neurological diseases (9). (TGGAA) n repeats, for example, may form noncanonical structures such as a hairpin arm (10, 11) or an antiparallel duplex (12). Expansion of this pentanucleotide sequence has been associated with spinocerebellar ataxia 31 (SCA31), an adult-onset autosomal-dominant neurodegenerative disorder (13).In this article, we probed the conformational heterogeneity and stability of hairpins composed of repetitive TGGAA sequences using single-molecule fluorescence resonance energy transfer [single-molecule FRET (smFRET)] spectroscopy and X-ray crystallography as primary tools. Remarkably, we were able to detect two distinct hairpin confi...