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Introduction: While minimal residual disease (MRD) negativity is not yet an established regulatory surrogate for a clinical endpoint in multiple myeloma (MM), it does have value as a prognostic biomarker and in assessing disease status. Previously we reported results from a phase 1b trial that described the safety and efficacy of the triplet regimen carfilzomib (given weekly), lenalidomide, and dexamethasone (KRd) in patients with relapsed and/or refractory MM (RRMM) or newly diagnosed MM (NDMM) (Biran et al, Am J Hematol 2019;94:794-802; Alsina et al, Clin Lymphoma Myeloma Leuk 2019;19:Suppl E52). Here, we evaluate MRD status by flow cytometry after treatment with weekly KRd in this trial. Methods: A total of 56 patients with RRMM and 51 with NDMM were enrolled and treated with weekly KRd. Treatment was given in 28-day cycles. Carfilzomib was given on days 1, 8, and 15; lenalidomide 25 mg on days 1-21; and dexamethasone 40 mg on days 1, 8, and 15 (also day 22 for cycle 1-8). In the NDMM cohort, patients were enrolled regardless of transplant eligibility, and treatment interruption for mobilization and collection with or without autologous stem cell transplant was allowed after cycle 4. Per the protocol, aspirate was collected for flow cytometry evaluation at two separate endpoints: at cycle 8 day 1 (C8D1); and at the time when laboratory data supported a response of complete response (CR) or better (on the basis of negative immunofixation on serum and urine). Sample quality was assessed by several measures (including the presence of mast cells, erythroid precursors, and immature B cells), and viability was determined using a flow assay. Adequate samples were tested for MRD using 8-color flow cytometry in two tubes, with a sensitivity of 10-5. MRD was reported as positive when a minimum of 2 x 106 CD138+ cells per tube were evaluated, and ≥ 20 abnormal events detected. Results: Overall, 58 of 79 (73.4%) study-specified samples were obtained and evaluated by flow cytometry. Of the NDMM patients, 15 had bone marrow aspirate evaluable for MRD at C8D1 (in total 22 patients were treated to C8D1), and 12 had bone marrow aspirate evaluable for MRD at the time of CR (14 patients achieved CR). At C8D1, 53% (8/15) of NDMM patients with flow data achieved MRD negativity, and at time of CR, 83% (10/12) of NDMM patients were MRD negative (the remaining patients with flow data were determined to be MRD positive). Among the 12 NDMM patients evaluated for MRD at time of CR, 17% had high-risk cytogenetics, 58% had standard-risk cytogenetics, and 25% had unknown cytogenetic risk status. Of the RRMM patients, 26 had bone marrow aspirate evaluable for MRD at C8D1 (30 patients were treated to C8D1), and five had bone marrow aspirate evaluable for MRD at the time of suspected CR or better (in total 13 patients achieved CR). Of RRMM patients with available flow data at time of CR, 40% (2/5) achieved MRD negativity, and of those with flow data at C8D1, 50% (13/26) achieved MRD negativity. Of all patient samples evaluated for MRD, 67% of NDMM and 48% of RRMM samples were MRD negative. The results reported here are directionally comparable to the rates of MRD-negative CRs observed in previous studies of twice-weekly KRd in NDMM (Jasielec J et al, Blood 2014;124:2127; Kazandjian D et al, JAMA Oncol 2018;4:1781-1783; Zimmerman T et al, Blood 2016;128:675). Our findings are limited by incomplete acquisition of samples to support a full MRD analysis per protocol (approximately 73% of the intended time point samples were acquired). Additionally, we reported MRD status without censoring for missing MRD data, as would be required to analyze MRD for a randomized controlled trial to eliminate acquisition bias. A robust comparison of MRD-negative CR rates between regimens would require an RCT with full MRD sampling, and sensitivity analyses that treat missing MRD data as MRD-positive (Chari A et al, Blood 2017;130:974-981; Voorhees PM et al, Blood 2020). Conclusions: We have previously shown that once-weekly KRd is active and has acceptable toxicity in both the RRMM and NDMM settings. We found that among MRD-evaluable patients who had a CR or better, MRD negativity rates were impressive in both the NDMM setting (83%) and in the RRMM setting (40%), suggesting that the weekly KRd regimen can induce MRD-negative CRs in both settings. Disclosures Landgren: Adaptive: Consultancy, Honoraria; Takeda: Other: Independent Data Monitoring Committees for clinical trials, Research Funding; Janssen: Consultancy, Honoraria, Other: Independent Data Monitoring Committees for clinical trials, Research Funding; Juno: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria; Janssen: Consultancy, Honoraria, Other: Independent Data Monitoring Committees for clinical trials, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; BMS: Consultancy, Honoraria; Cellectis: Consultancy, Honoraria; Merck: Other; Cellectis: Consultancy, Honoraria; Binding Site: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Amgen: Consultancy, Honoraria, Research Funding; Merck: Other; BMS: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria; Seattle Genetics: Research Funding; Glenmark: Consultancy, Honoraria, Research Funding; Binding Site: Consultancy, Honoraria; Karyopharma: Research Funding; Takeda: Other: Independent Data Monitoring Committees for clinical trials, Research Funding; Juno: Consultancy, Honoraria; Glenmark: Consultancy, Honoraria, Research Funding; Karyopharma: Research Funding; Seattle Genetics: Research Funding. Alsina:Janssen: Honoraria, Speakers Bureau; BMS: Consultancy, Research Funding; Celgene: Consultancy, Honoraria; Amgen: Honoraria, Speakers Bureau. Biran:Janssen: Consultancy, Honoraria, Other: reimbursement of travel and accomodation, Research Funding, Speakers Bureau; KAryopharma: Research Funding; Sanofi: Honoraria, Speakers Bureau; Amgen: Consultancy, Honoraria, Other: reimbursement of travel and accomodation, Research Funding, Speakers Bureau; BMS: Consultancy, Honoraria, Other: reimbursement of travel and accommodation, Research Funding, Speakers Bureau. Vesole:Amgen: Speakers Bureau; Takeda: Speakers Bureau; Sanofi: Speakers Bureau; Janssen: Speakers Bureau; BMS: Speakers Bureau. Fang:Amgen: Current Employment, Current equity holder in publicly-traded company. Arnold:Amgen: Current Employment, Current equity holder in publicly-traded company. Kimball:Amgen: Current Employment, Current equity holder in publicly-traded company; WindMIL Therapeutics: Current equity holder in private company. Siegel:Karyopharma: Consultancy, Honoraria; Takeda: Consultancy, Honoraria, Speakers Bureau; BMS: Consultancy, Honoraria, Speakers Bureau; Janssen: Consultancy, Honoraria, Speakers Bureau; Merck: Consultancy, Honoraria, Speakers Bureau; Amgen: Consultancy, Honoraria, Speakers Bureau; Celulatiry: Consultancy. OffLabel Disclosure: Carfilzomib is a proteasome inhibitor that can be used for the treatment of relapses/refractory multiple myeloma

Objective To assess the safety and immunologic impact of inhibiting interferon-γ (IFNγ) with AMG 811, a human IgG1 monoclonal antibody against IFNγ, in patients with systemic lupus erythematosus (SLE). Methods Twenty-six patients with mild-to-moderate, stable SLE were administered placebo or a single dose of AMG 811, ranging from 2 mg to 180 mg subcutaneously or 60 mg intravenously. Results Similar to results previously reported following inhibition of type I IFNs, treatment of SLE patients with AMG 811 led to a dose-dependent modulation of the expression of genes associated with IFN signaling, as assessed by microarray analysis of the whole blood. The list of impacted genes overlapped with that identified by stimulating human whole blood with IFNγ and with those gene sets reported in the literature to be differentially expressed in SLE patients. Serum levels of IFNγ-induced chemokines, including IFNγ-inducible protein 10 (IP-10), were found to be elevated at baseline in SLE patients as compared to healthy volunteers. In contrast to previously reported results from studies using type I IFN–blocking agents, treatment with AMG 811 led to dose-related reductions in the serum levels of CXCL10 (IP-10). Conclusion The scope and nature of the biomarkers impacted by AMG 811 support targeting of IFNγ as a therapeutic strategy for SLE.

Background Blockade of inducible costimulatory ligand (ICOSL) might be a promising approach for autoimmune diseases such as systemic lupus erythematosus (SLE). We evaluated AMG 557, an anti-ICOSL monoclonal antibody, in an exploratory phase 1b study of SLE subjects with inflammatory arthritis, by withdrawing background therapies to improve interpretability of a small study. Objectives To investigate potential efficacy, safety, and tolerability of AMG 557 in subjects with lupus arthritis. Methods This double-blind, randomized, placebo-controlled trial enrolled subjects with SLE and active lupus arthritis (≥4 tender and 4 swollen joints) and Systemic Lupus Erythematosus Disease Activity Index [SLEDAI] score ≥6 despite stable background immunosuppressants. Upon enrollment, investigators were permitted to use up to 20 mg/day of prednisone, which was tapered by day 85 to 7.5 mg/day or 50% of baseline, whichever was lower. Subjects received AMG 557 210 mg or placebo once weekly for 3 weeks followed by 10 additional doses every other week until day 155. At day 29, background immunosuppressants were withdrawn. The primary clinical endpoint was a composite Lupus Arthritis Responder Index at day 169; response was defined as achieving: (1) 50% decrease in combined tender and swollen joint counts, and (2) ≥1 letter improvement in the musculoskeletal subsystem of the British Isles Lupus Assessment Group (BILAG) index and (3) prespecified immunosuppressant medication withdrawal and/or prednisone taper. Safety was a co-primary endpoint. Exploratory endpoints included safety, 4-point reduction of SLEDAI, clinical indices (SLEDAI, BILAG), complement components, autoantibodies, and lymphocyte populations. Results Twenty subjects (19 females) were randomized (10 AMG 557, 10 placebo) at 8 sites in North America, Asia, and Europe. The primary endpoint was met by 3/10 subjects receiving AMG 557 and 1/10 subjects receiving placebo ( P =ns). A 4-point decrease in SLEDAI score was achieved by 7/10 subjects on AMG 557 and 2/10 subjects on placebo. At day 169, subjects receiving AMG 557 had decreases from baseline in mean global BILAG and SLEDAI scores of 36% and 48% respectively, compared to 25% and 11% in subjects receiving placebo. Lupus-associated biomarkers, including serum complement indices (C3, C4, and CH50), and autoantibodies, including anti-dsDNA, demonstrated trends towards improvement relative to placebo. Treatment-emergent adverse events (AEs) were similar between placebo and AMG 557 arms; most commonly headache and upper respiratory tract infection. Conclusions Results from this exploratory placebo-controlled trial in lupus arthritis suggest potential clinical benefit of ICOSL blockade by AMG 557. These data support further clinical trials intervening in this costimulatory pathway in SLE and other autoimmune diseases. Disclosure of Interest L. Cheng Shareholder of: Amgen Inc., Employee of: Amgen Inc., Z. Amoura Consultant for: GlaxoSmithKline, AstaZeneca, BristolMyerSquibb, Amgen Inc., B. Cheah Grant/research support from: Merck, F. Hiepe Grant/research support from: Sanofi, Amgen Inc., GlaxoSmithKline, AstaZeneca, Ablynx, Consultant for: Baxalta, AstaZeneca, BristolMyerSquibb, GlaxoSmithKline, Novartix, Miltenyi, Neovacs, Hexal, Neovi, Speakers bureau: Pfizer Inc., Roche, UCB, B. Sullivan Shareholder of: Amgen Inc., Employee of: Amgen Inc., L. Zhou Shareholder of: Amgen Inc., Employee of: Amgen Inc., G. Arnold Shareholder of: Amgen Inc., Employee of: Amgen Inc., W. Tsuji Shareholder of: Amgen Inc., JohnsonJ Partner in the Cascadia Drug Development Group, J. Merrill Consultant for: EMD Serono, BristolMyerSquibb, Human Genome Sciences, UCB, AstraZeneca, Celgene, J. Chung Shareholder of: Amgen Inc., Employee of: Amgen Inc.

Objective Interferon-γ (IFNγ) is implicated in the pathogenesis of discoid lupus erythematosus (DLE). This study sought to evaluate a single dose of AMG 811, an anti-IFNγ antibody, in patients with DLE. Methods The study was designed as a phase I randomized, double-blind, placebo-controlled crossover study of the pharmacodynamics, safety, and clinical efficacy of AMG 811 in patients with DLE. Patients received a single subcutaneous dose of AMG 811 (180 mg) or placebo. The patients in sequence 1 received AMG 811 followed by placebo, while those in sequence 2 received placebo followed by AMG 811. Pharmacodynamic end points included global transcriptional analyses of lesional and nonlesional skin, IFNγ blockade signature (IGBS) transcriptional scores in the skin and blood, keratinocyte IFNγ RNA scores, and serum levels of CXCL10 protein. Additional end points were efficacy outcome measures, including the Cutaneous Lupus Erythematosus Disease Area and Severity Index, and safety outcome measures. Results Sixteen patients with DLE were enrolled in the study (9 in sequence 1 and 7 in sequence 2). AMG 811 treatment reduced the IGBS score (which was elevated in DLE patients at baseline) in both the blood and lesional skin. The keratinocyte IFNγ RNA score was not affected by administration of AMG 811. Serum CXCL10 protein levels (which were elevated in the blood of DLE patients) were reduced with AMG 811 treatment. The AMG 811 treatment was well tolerated but did not lead to statistically significant improvements in any of the efficacy outcome measures. Conclusion AMG 811 treatment led to changes in IFNγ-associated biomarkers and was well tolerated, but no significant clinical benefit was observed in patients with DLE.

Objective To evaluate safety, pharmacokinetics and pharmacodynamics of anti-interferon (IFN)-γ monoclonal antibody AMG 811 in subjects with SLE without or with lupus nephritis (LN). Methods In this phase Ib, randomised, multiple-dose escalation study (NCT00818948), subjects without LN were randomised to subcutaneous AMG 811 (6, 20 or 60 mg) or placebo and subjects with LN were randomised to subcutaneous AMG 811 (20, 60 or 120 mg) or placebo every four weeks for three total doses. Outcomes included incidence of adverse events (AEs); pharmacokinetics; levels of serum proteins (CXCL-10, interleukin 18, monocyte chemotactic protein-1); changes in gene transcript profiles and clinical parameters (Safety of Estrogen in Lupus Erythematosus National Assessment-Systemic Lupus Erythematosus Disease Activity Index (SELENA-SLEDAI) scores, proteinuria, anti-double-stranded DNA (anti-dsDNA) antibodies, C3 complement, C4 complement). Results Fifty-six subjects enrolled (28 SLE without LN; 28 with LN). Baseline mean SELENA-SLEDAI scores were 2.2 and 12.0 for SLE subjects without and with LN, respectively. Most subjects reported an AE; no meaningful imbalances were observed between AMG 811 and placebo. Pharmacokinetic profiles were similar and mostly dose-proportional in subjects without or with LN. AMG 811 treatment reduced CXCL-10 protein levels and blood-based RNA IFN-γ Blockade Signature compared with placebo. Reductions were less pronounced and not sustained in subjects with LN, even at the highest dose tested, compared with subjects without LN. No effect on SELENA-SLEDAI scores, proteinuria, C3 or C4 complement levels, or anti-dsDNA antibodies was observed. Conclusion AMG 811 demonstrated favourable pharmacokinetics and acceptable safety profile but no evidence of clinical impact. IFN-γ-associated biomarkers decreased with AMG 811; effects were less pronounced and not sustained in LN subjects. Trial registration number NCT00818948; results.

A dynamical model of interdomain "hinge bending" of T4 lysozyme in aqueous solution has been developed on the basis of molecular dynamics (MD) simulation. The MD model study provides a description of the conformational reorganization expected to occur for the protein in aqueous solution as compared to the crystalline environment. Three different 500 ps molecular dynamics simulations were calculated, each using a distinctly different crystal conformation of T4 lysozyme as the starting points of the MD simulations. Crystal structures of wild-type lysozyme and "open" and "closed" forms of M61 variant structures were analyzed in this study. Large-scale, molecular-conformational rearrangements were observed in all three simulations, and the largest structural change was found for the open form of the M61 allomorph. All three simulated proteins had closed relative to the wild-type crystal structure, and the closure of the "jaws" of the active site cleft occurred gradually over the time course of the trajectories. The time average MD structures, calculated over the final 50 ps of each trajectory, had all adapted to conformations more similar to each other than to their incipient crystal forms. Using a similar MD protocol on cytochrome P450BM-3 [M. D. Paulsen and R. L. Ornstein (1995) Proteins: Structure Function and Genetics, Vol. 27, pp. 237-243] we have found that the opposite type of motion relative to the starting crystal structure, that is, the open form of the crystal structure, had opened to a greater degree relative to the incipient crystal structure form. Therefore we do not believe that either result is merely a simulation artifact, but rather the protein dynamics are due to protein relaxation in the absence of crystal packing forces in the simulated solution environments.

The stereoselectivity of cytochrome P450cam hydroxylation has been investigated with the enantiomerically pure substrate analog norcamphor. (1R)- and (1S)-norcamphor (> 92 enantiomeric excess) were characterized in the hydroxylation reaction with cytochrome P450cam with respect to the product profile, steady state kinetics, coupling efficiency, and free energy of substrate dissociation. The experimental results demonstrate regiospecificity that is enantiomer-specific and confirm our previously reported prediction that (1R)-norcamphor is hydroxylated preferentially at the 5-carbon and (1S)-norcamphor at the 6-carbon (Bass, M. B., and Ornstein, R. L. (1993) J. Comput. Chem. 14, 541-548); these simulation results are now compared with simulations involving a ferryl oxygen intermediate. Hydroxylation of (1R)-norcamphor was found at the 5-, 6-, and 3-carbons in a ratio of 65:30:5 (respectively), whereas (1S)-norcamphor was oxidized to produce a 28:62:10 ratio of the same products. With the exception of the regiospecificity, all of the reaction and physical parameters are similar for each enantiomer of norcamphor. These results show that the position of the carbonyl group on the hydrocarbon skeleton of norcamphor plays a role in determining the average orientation of this substrate in the active site and suggests that hydrogen bonding interactions can aid in directing the regiospecificity and stereospecificity of the hydroxylation reaction catalyzed by cytochrome P450cam.

In this report we examine several solvent models for use in molecular dynamics simulations of protein molecules with the Discover program from Biosym Technologies. Our goal was to find a solvent system which strikes a reasonable balance among theoretical rigor, computational efficiency, and experimental reality. We chose phage T4 lysozyme as our model protein and analyzed 14 simulations using different solvent models. We tested both implicit and explicit solvent models using either a linear distance-dependent dielectric or a constant dielectric. Use of a linear distance-dependent dielectric with implicit solvent significantly diminished atomic fluctuations in the protein and kept the protein close to the starting crystal structure. In systems using a constant dielectric and explicit solvent, atomic fluctuations were much greater and the protein was able to sample a larger portion of conformational space. A series of nonbonded cutoff distances (9.0, 11.5, 15.0, 20.0 A) using both abrupt and smooth truncation of the nonbonded cutoff distances were tested. The method of dual cutoffs was also tested. We found that a minimum nonbonded cutoff distance of 15.0 A was needed in order to properly couple solvent and solute. Distances shorter than 15.0 A resulted in a significant temperature gradient between the solvent and solute. In all trajectories using the proprietary Discover switching function, we found significant denaturation in the protein backbone; we were able to run successful trajectories only in those simulations that used no switching function. We were able to significantly reduce the computational burden by using dual cutoffs and still calculate a quality trajectory. In this method, we found that an outer cutoff distance of 15.0 A and an inner cutoff distance of 11.5 worked well. While a 10 A shell of explicit water yielded the best results, a 6 A shell of water yielded satisfactory results with nearly a 40% reduction in computational cost.

An analysis of a 400 ps molecular dynamics simulation of the 164 amino acid enzyme T4 lysozyme is presented. The simulation was carried out with all hydrogen atoms modeled explicitly, the inclusion of all 152 crystallographic waters and at a temperature of 300 K. Temporal analysis of the trajectory versus energy, hydrogen bond stability, r.m.s. deviation from the starting crystal structure and radius of gyration, demonstrates that the simulation was both stable and representative of the average experimental structure. Average structural properties were calculated from the enzyme trajectory and compared with the crystal structure. The mean value of the C alpha displacements of the average simulated structure from the X-ray structure was 1.1 +/- 0.1 A; differences of the backbone phi and psi angles between the average simulated structure and the crystal structure were also examined. Thermal-B factors were calculated from the simulation for heavy and backbone atoms and both were in good agreement with experimental values. Relationships between protein secondary structure elements and internal motions were studied by examining the positional fluctuations of individual helix, sheet and turn structures. The structural integrity in the secondary structure units was preserved throughout the simulation; however, the A helix did show some unusually high atomic fluctuations. The largest backbone atom r.m.s. fluctuations were found in non-secondary structure regions; similar results were observed for r.m.s. fluctuations of non-secondary structure phi and psi angles. In general, the calculated values of r.m.s. fluctuations were quite small for the secondary structure elements. In contrast, surface loops and turns exhibited much larger values, being able to sample larger regions of conformational space. The C alpha difference distance matrix and super-positioning analyses comparing the X-ray structure with the average dynamics structure suggest that a 'hinge-bending' motion occurs between the N- and C-terminal domains.

Background Interferon-gamma (IFN-g) is a pro-inflammatory cytokine that modulates the function of several important immune populations. Evidence from human and animal models suggests that increased levels of Type I and/or Type II IFN are associated with SLE. Objectives This study assessed the safety, tolerability, PK and pharmacodynamic (PD) data from AMG 811, an anti-IFNg mAb, in subjects with active class III or IV LN. Methods Subjects were enrolled if they had new onset or reactivation of biopsy-proven (within 18 months) class III or IV LN, UP/Cr >1 or 24 hr urine protein >1 g after at least 12 wks of treatment with MMF or AZA. Superimposed membranous changes were allowed. Subjects with rapidly progressive GN or significant chronicity were excluded. Subjects could receive oral prednisone at doses up to 20 mg/day. Subjects were randomized to placebo or ascending doses of AMG 811 (20, 60 or 120 mg given SC q4 wks for three doses at 3:1 allocation) in addition to MMF or AZA. The primary endpoints were safety, tolerability, and anti-drug antibodies. Serum AMG 811 concentrations, anti-AMG 811 antibodies and PD biomarkers (blood RNA and serum) were also assessed. Disease related assessments included reduction from baseline in proteinuria (24 hr urine and spot UP/Cr), SLEDAI scores and changes in SLE-related biomarkers. Results 28 subjects were enrolled: 7 in the PBO group and 21 in the AMG 811 treatment groups. The proportion of subjects reporting treatment emergent AEs, including serious AEs, was similar between PBO and AMG 811 groups although a numerically higher proportion of subjects treated with AMG 811 had infectious events. AMG 811 displayed linear PK with half-life of 11-21 days. Exposures after doses of 20 & 60 mg in LN subjects were similar to exposures in non-renal SLE subjects. Antibodies to AMG 811 were not observed at any time. Baseline serum CXCL10 (IP-10) levels and IFNgamma-modulated mRNAs were higher in LN compared to non-renal SLE; both populations had elevated levels compared to healthy controls. AMG 811 (60 & 120 mg cohorts) led to a reduction in these biomarkers, albeit incomplete and transient, suggesting that AMG 811 may have had reduced target coverage in LN relative to non-renal SLE, where levels were reduced into the healthy range. Although numerous subjects demonstrated improvement in proteinuria, no consistent differences between AMG 811 treatment cohorts and PBO were discernable at week 12 in renal outcome or SLE-related serum biomarkers. Conclusions AMG 811 demonstrated a favorable PK and immunogenicity profile in active LN subjects, and the overall safety profile was acceptable in this small study. Inhibition of pharmacodynamic biomarkers with doses up to 120 mg of AMG 811 appeared incomplete in LN subjects. There were no discernible effects of AMG 811 on clinical or SLE-related serologic outcome measures over the treatment period although interpretation is challenging given the small sample size. Disclosure of Interest D. Martin Employee of: Amgen, Z. Amoura: None declared, J. Romero-Diaz: None declared, Y. Chong: None declared, J. Sanchez-Guerrero: None declared, T. Chan: None declared, G. Arnold Employee of: Amgen, M. Damore Employee of: Amgen, W. Sohn Employee of: Amgen, N. Chirmule Employee of: Amgen, K. Chiu Employee of: Amgen, C. Wang Employee of: Amgen, M. Boedigheimer Employee of: Amgen, B. Sullivan Employee of: Amgen, A. Welcher Employee of: Amgen, B. Kotzin Employee of: Amgen, J. Chung Employee of: Amgen

Interaction of fd or M13 filamentous phage with a chloroform/water interface induces morphological change, contracting the filaments sequentially into shortened rods (I-forms), and then into spheroidal particles (S-forms). To further investigate this phage contraction, 34 and 26 chloroform-resistant isolates of fd and M13, respectively, were selected after chloroform treatment of wild-type phages at pH 8. 2 and 4 degrees C. DNA sequencing of gene VIII of the 34 fd isolates revealed five different mutants: these were D5H, M28L, V31L, I37T, and S50T. All 26 M13 isolates were I37T. These mutants exhibited variable sensitivity to chloroform, but all contracted much more slowly than wild-type phage during treatment at 4 degrees C. They all contracted like wild-type phage at 37 degrees C. Site-directed mutagenesis showed that the indicated single mutations carried the chloroform resistance. In structural models of the phage, the D5H locus is on the outside and the S50T locus is on the inside. The M28L and I37T loci are buried in a mostly hydrophobic region in the middle. Although these four mutants are spread out radially, they are localized in the axial direction into a thin disk in the model. The last mutant locus, V31L, is out of this disk, but this locus is proximal to the M28L and I37T loci and also in contact with the surface via a deep hydrophobic hole or depression. These five mutants, their locations, and their variable affects on contraction suggest that chloroform-induced contraction involves a specific mechanism rather than a generalized solvent-induced denaturation and that the critical structural changes occur in a localized level in the phage. These results add weight to suggestions that the sequential contraction of filaments-->I-forms-->S-forms mimic corresponding steps in phage penetration, and, in the reverse order, for phage assembly.

Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises an important question: are the different conformers in the unit cell artifacts of crystal packing forces, or do they represent different solution state structures? The objective of this theoretical study is to determine whether domain motions and hinge-bending could be simulated in T4 lysozyme using molecular dynamics. An analysis of a 400 ps molecular dynamics simulation of the 164 amino acid enzyme T4 lysozyme is presented. Molecular dynamics calculations were computed using the Discover software package (Biosym Technologies). All hydrogen atoms were modeled explicitly with the inclusion of all 152 crystallographic waters at a temperature of 300 K. The native T4 lysozyme molecular dynamics simulation demonstrated hinge-bending in the protein. Relative domain motions between the N-terminal and C-terminal domains were evident. The enzyme hinge bending sites resulted from small changes in backbone atom conformations over several residues rather than rotation about a single bound. Two hinge foci were found in the simulation. One locus comprises residues 8-14 near the C-terminal of the A helix; the other site, residues 77-83 near the C-terminal of the C helix. Comparison of several snapshot structures from the dynamics trajectory clearly illustrates domain motions between the two lysozyme lobes. Time correlated atomic motions in the protein were analyzed using a dynamical cross-correlation map. We found a high degree of correlated atomic motions in each of the domains and, to a lesser extent, anticorrelated motions between the two domains. We also found that the hairpin loop in the N-terminal lobe (residues 19-24) acted as a mobile 'flap' and exhibited highly correlated dynamic motions across the cleft of the active site, especially with residue 142.

Abstract 1303 Studies of the regulation of erythropoiesis by hypoxic induction of erythropoietin (EPO) transcription led to the discovery of oligonucleotide binding motifs, hypoxia responsive elements (HREs) essential for hypoxic upregulation of EPO. HREs bind hypoxia-inducible transcription factors (HIFs). HIFs are heterodimers of 3 α subunit isotypes; HIF-1α, HIF-2α, and HIF-3α, and a common β-subunit. EPO is expressed in diverse tissues, some regulated mainly by HIF-2 and others by HIF-1. Tissue-specific regulatory elements (i.e. Kidney Inducible Element KIE, Negative Regulatory Element NRE, and Negative Regulatory Liver specific Element NRLE) of the EPO gene spanning several kilobases were reported. Our in silico analysis of the human EPO genome found two additional canonical HIF-binding elements in the KIE and NRE regions, and comparative analysis of phylogenically conserved sequences of Epo genes refined these HIF-binding elements from several kbs to a few hundred nucleotides and further delineated them as mKIE, mNRE1, mNRE2, and mNRLE2. To further define the structure and function of these elements in vivo, we exposed mice to 8% O2 hypoxia and monitored hypoxic induction of Epo mRNA levels in the liver, kidney, brain, and spleen. Spleen, kidney, and brain had a peak induction of the Epo transcript at 3 hours of hypoxia treatment, while liver showed peak induction at 6 hours. At the end of the hypoxia treatment, the mice were sacrificed and organs were harvested, and in vivo chromatin immunoprecipitation (ChIPs) was performed with antibodies against HIF-1α and HIF-2α. The results from these studies are summarized below. “+” denotes presence and “−” absence of binding of HIF-1 and HIF-2. “Norm” - normoxia, “Hyp” - hypoxia. To further define the role of these elements in tissue-specific Epo expression, we cloned and mutated these elements with reporter constructs, and generated transgenic mouse strains. The reporter gene was expressed in renal tubules, the red pulp area of the spleen, and liver hepatocytes. By creating a designed point mutation to disrupt the function of KIE, we suppressed the hypoxia response in the kidney, while mutations of NRE1 and NRE2 abolished reporter expression in the liver. Studies of HREs in the brain are ongoing. In conclusion, we have refined the previously reported HREs to a few hundred bases (particularly, KIE is a 6 nucleotide bearing motif) and now demonstrate tissue-specific differential hypoxia-induced binding of HIF-1 and HIF-2 and their functional roles in EPO induction. This provides a background to examine the molecular basis of these elements in patients with aberrant EPO expression. Disclosures: Elliott: Amgen, Inc: Employment.

The conditional probability, P(sigma/x), is a statement of the probability that the value of sigma will be found given the prior information that a value of x has been observed. Here sigma represents any one of the secondary structure types, alpha, beta, tau, and rho for helix, sheet, turn, and random, respectively, and x represents a sequence attribute, including, but not limited to: (1) hydropathy; (2) hydrophobic moments assuming helix and sheet; (3) Richardson and Richardson helical N-cap and C-cap values; (4) Chou-Fasman conformational parameters for helix, P alpha, for sheet, P beta, and for turn, P tau; and (5) Garnier, Osguthorpe, and Robson (GOR) information values for helix, I alpha, for sheet, I beta, for turn, I tau, and for random structure, I rho. Plots of P(sigma/x) vs. x are demonstrated to provide information about the correlation between structure and attribute, sigma and x. The separations between different P(sigma/x) vs. x curves indicate the capacity of a given attribute to discriminate between different secondary structural types and permit comparison of different attributes. P(alpha/x), P(beta/x), P(tau/x) and P(rho/x) vs. x plots show that the most useful attributes for discriminating helix are, in order: hydrophobic moment assuming helix greater than P alpha much greater than N-cap greater than C-cap approximately I alpha approximately I tau. The information value for turns, I tau, was found to discriminate helix better than turns. Discrimination for sheet was found to be in the following order: I beta much greater than P beta approximately hydropathy greater than I rho approximately hydrophobic moment assuming sheet. Three attributes, at their low values, were found to give significant discrimination for the absence of helix: I alpha approximately P alpha approximately hydrophobic moment assuming helix. Also, three other attributes were found to indicate the absence of sheet: P beta much greater than I rho approximately hydropathy. Indications of the absence of sigma could be as useful for some applications as the indication of the presence of sigma.

The fd filamentous phage can be contracted to short rods called I-forms and to spheroidal particles called S-forms. The conversions from fd→I-forms→S-forms were previously suggested to mimic steps in fd penetration. The same conversions, in reverse order, were suggested to mimic steps in fd assembly. The I-forms and S-forms bind the hydrophobic probe, 1-anilino-napthalene-8-sulionate (ANS); under the same conditions, fd binds this probe very poorly. Rigidly packed side chains in fd and nonrigidly packed side chains in I-forms and S-forms would explain the differences in ANS binding. A compilation of the properties of I-forms and S-forms indicate that: (i) they have compact structures; (ii) they have secondary structures of the same type as native phage; (iii) they have non-native morphologies; and (iv) they may have nonrigid side chain packing. These are the properties of molten globules.

Hypoxia regulates erythropoiesis and other essential processes via hypoxia-inducible transcription factors (HIFs). HIFs are heterodimers that consist of an α subunit (3 isotypes with significant homology; HIF-1α, HIF-2α, HIF-3α), and a common b-subunit; HIF-1 and HIF-2, in some instances exhibiting tissue- and gene-specific gene regulation. Erythropoietin (EPO) was the first identified HIF-1 target gene with the defined HIF-1 binding sequence. However, subsequent works suggested that HIF-2 also regulates EPO transcription and that there are other regulatory elements of EPO gene (i.e. Kidney Inducible Element KIE, Negative Regulatory Element NRE, and Negative Regulatory Liver specific Element NRLE). In silico analysis of the human EPO genome found two additional potential HIF-binding elements in the KIE and NRE regions. The comparative analysis of phylogenically conserved sequences of human, mouse, dog, and rat Epo genes further refined these mouse Epo gene HIF-binding elements as mKIE, mNRE1, mNRE2, and mNRLE2. We treated mice in hypoxia chamber (8% O2) and monitored changes of Epo mRNA levels in liver, kidney, brain, spleen, and bone marrow. All tested tissues increased Epo transcription during hypoxia. Bone marrow, spleen, kidney, and brain showed a peak of induction of Epo transcript at 3 hours of hypoxia treatment, while liver reached the highest level at 6 hours. Mice were sacrificed and organs were harvested, and in vivo chromatin immunoprecipitation (ChIPs) was performed with antibodies against HIF-1α and HIF- 2α and tissue-specific binding regions were defined. The results from these studies are summarized below. HIF-1 mKIE rnNRE mNRE2 mNRLE2 Norm Hyp Norm Hyp Norm Hyp Norm Hyp Liver − + − − + − ? ? Kidney − + − − + − + − Brain − + − − − + − + BM − + − − − − − + Splsen − + − − − − − + HIF-2 mKIE mNRE mNRE2 mNRLE2 Norm Hyp Norm Hyp Norm Hyp Norm Hyp Liver − + − − − + − + Kidney + − − − + − ? ? Brain − − − − − − − + BM − − − − − − + − Spleen − + − − − − − + “+” denotes presence and “-” absence of binding of HIF-1 and HIF-2, “?” – indicates inconclusive results. “Norm” - normoxia, “Hyp” - hypoxia. In conclusion, we demonstrate the differential hypoxia-induced binding of HIF-1 and HIF-2 at different HIF binding elements in the tissues known to express Epo. Further studies will be required to define the function of these HIF-1 and HIF-2 binding elements in tissue specific Epo expression and their role in health and disease.

Following irradiation of human cells with ultraviolet light, DNA repair patches are initially inserted near the 5' and 3' ends of nucleosome core DNA leaving a "gap" in repair synthesis (of approximately 50 bases) near the center of the core DNA. With time, however, these same repair patches become randomized, apparently by nucleosome migration. We have developed both an analytical expression and a computer algorithm (which simulates nucleosome migration along DNA) to determine the average distance nucleosomes must migrate to change the initial, non-uniform distribution of repair patches in nucleosomes to a random distribution. Both of these methods yielded the same result: nucleosomes must migrate an average of about 50 base-pairs in either direction to produce the randomization observed.