Computational Studies of E. coli DHFR: Drug Design, Dynamics, and Method Development.

Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate. As the only source of tetrahydrofolate (an important precursor in the biosynthesis of purines, thymidylate, and several amino acids), it has been a long-standing anti-cancer target and a classic system for structure-based drug design (SBDD). Escherichia coli DHFR (ecDHFR) is a canonical system for studying enzyme structure, dynamics, and catalysis. Protein flexibility and dynamics are of utmost importance in understanding the structure and mechanism of DHFR. This has been well investigated computationally and experimentally. The conformation of the M20 loop is particularly important to the catalytic cycle, as its three major conformations (open, closed, and occluded) are known to regulate ligand affinity and turnover. In addition to these static conformational differences, correlated dynamics are known to be of primary importance, showing distinct changes during different stages of the catalytic cycle. The dynamics have been used to explain the effects of distal mutations. We have performed two 10-ns molecular dynamics simulations of the ecDHFR•NADPH complex. We discovered transient, sub-nanosecond, correlated dynamics that correspond to correlations found in the catalytically active state. These dynamics involve both the protein and the cofactor. We found conformational changes that clearly indicate preorganization of the binding site related to folate binding. We have also discovered a potential new allosteric site, supported by extensive computational work as well as by crystallographic and mutagenesis results in the literature. Traditional SBDD techniques focus on static structures. In 1999, Carlson and coworkers introduced the MPS (multiple protein structure) method as a way of incorporating protein flexibility into SBDD. The extreme importance of flexibility for DHFR makes the MPS method particularly appropriate. To improve the method, we developed new techniques for flooding and automatically clustering the solvent-mapping probes used in the procedure. We generated models from simulations starting with the M20 loop in both open and closed conformations. The MPS models preferentially identified high-affinity inhibitors over drug-like non-inhibitors.Ph.D.BiophysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/58475/1/mlerner_1.pd

Determination of biomembrane bending moduli in fully atomistic simulations.

The bilayer bending modulus (Kc) is one of the most important physical constants characterizing lipid membranes, but precisely measuring it is a challenge, both experimentally and computationally. Experimental measurements on chemically identical bilayers often differ depending upon the techniques employed, and robust simulation results have previously been limited to coarse-grained models (at varying levels of resolution). This Communication demonstrates the extraction of Kc from fully atomistic molecular dynamics simulations for three different single-component lipid bilayers (DPPC, DOPC, and DOPE). The results agree quantitatively with experiments that measure thermal shape fluctuations in giant unilamellar vesicles. Lipid tilt, twist, and compression moduli are also reported

Comment on Higgs Inflation and Naturalness

We rebut the recent claim (arXiv:0912.5463) that Einstein-frame scattering in the Higgs inflation model is unitary above the cut-off energy Lambda ~ Mp/xi. We show explicitly how unitarity problems arise in both the Einstein and Jordan frames of the theory. In a covariant gauge they arise from non-minimal Higgs self-couplings, which cannot be removed by field redefinitions because the target space is not flat. In unitary gauge, where there is only a single scalar which can be redefined to achieve canonical kinetic terms, the unitarity problems arise through non-minimal Higgs-gauge couplings.Comment: 5 pages, 1 figure V3: Journal Versio

Quantum Phase and Quantum Phase Operators: Some Physics and Some History

After reviewing the role of phase in quantum mechanics, I discuss, with the aid of a number of unpublished documents, the development of quantum phase operators in the 1960's. Interwoven in the discussion are the critical physics questions of the field: Are there (unique) quantum phase operators and are there quantum systems which can determine their nature? I conclude with a critique of recent proposals which have shed new light on the problem.Comment: 19 pages, 2 Figs. taken from published articles, LaTeX, to be published in Physica Scripta, Los Alamos preprint LA-UR-92-352

AR2, a novel automatic muscle artifact reduction software method for ictal EEG interpretation: Validation and comparison of performance with commercially available software.

Objective: To develop a novel software method (AR2) for reducing muscle contamination of ictal scalp electroencephalogram (EEG), and validate this method on the basis of its performance in comparison to a commercially available software method (AR1) to accurately depict seizure-onset location. Methods: A blinded investigation used 23 EEG recordings of seizures from 8 patients. Each recording was uninterpretable with digital filtering because of muscle artifact and processed using AR1 and AR2 and reviewed by 26 EEG specialists. EEG readers assessed seizure-onset time, lateralization, and region, and specified confidence for each determination. The two methods were validated on the basis of the number of readers able to render assignments, confidence, the intra-class correlation (ICC), and agreement with other clinical findings. Results: Among the 23 seizures, two-thirds of the readers were able to delineate seizure-onset time in 10 of 23 using AR1, and 15 of 23 using AR2 (

Intravesical rAd-IFNα/Syn3 for Patients With High-Grade, Bacillus Calmette-Guerin-Refractory or Relapsed Non-Muscle-Invasive Bladder Cancer: A Phase II Randomized Study.

Purpose Many patients with high-risk non-muscle-invasive bladder cancer (NMIBC) are either refractory to bacillus Calmette-Guerin (BCG) treatment or may experience disease relapse. We assessed the efficacy and safety of recombinant adenovirus interferon alfa with Syn3 (rAd-IFNα/Syn3), a replication-deficient recombinant adenovirus gene transfer vector, for patients with high-grade (HG) BCG-refractory or relapsed NMIBC. Methods In this open-label, multicenter (n = 13), parallel-arm, phase II study ( ClinicalTrials.gov identifier: NCT01687244), 43 patients with HG BCG-refractory or relapsed NMIBC received intravesical rAd-IFNα/Syn3 (randomly assigned 1:1 to 1 × 10(11) viral particles (vp)/mL or 3 × 10(11) vp/mL). Patients who responded at months 3, 6, and 9 were retreated at months 4, 7, and 10. The primary end point was 12-month HG recurrence-free survival (RFS). All patients who received at least one dose were included in efficacy and safety analyses. Results Forty patients received rAd-IFNα/Syn3 (1 × 10(11) vp/mL, n = 21; 3 × 10(11) vp/mL, n = 19) between November 5, 2012, and April 8, 2015. Fourteen patients (35.0%; 90% CI, 22.6% to 49.2%) remained free of HG recurrence 12 months after initial treatment. Comparable 12-month HG RFS was noted for both doses. Of these 14 patients, two experienced recurrence at 21 and 28 months, respectively, after treatment initiation, and one died as a result of an upper tract tumor at 17 months without a recurrence. rAd-IFNα/Syn3 was well tolerated; no grade four or five adverse events (AEs) occurred, and no patient discontinued treatment because of an adverse event. The most frequently reported drug-related AEs were micturition urgency (n = 16; 40%), dysuria (n = 16; 40%), fatigue (n = 13; 32.5%), pollakiuria (n = 11; 28%), and hematuria and nocturia (n = 10 each; 25%). Conclusion rAd-IFNα/Syn3 was well tolerated. It demonstrated promising efficacy for patients with HG NMIBC after BCG therapy who were unable or unwilling to undergo radical cystectomy

Drag in paired electron-hole layers

We investigate transresistance effects in electron-hole double layer systems with an excitonic condensate. Our theory is based on the use of a minimum dissipation premise to fix the current carried by the condensate. We find that the drag resistance jumps discontinuously at the condensation temperature and diverges as the temperature approaches zero.Comment: 12 pages, 1 Figure, .eps file attache

Vacuum Stability, Perturbativity, and Scalar Singlet Dark Matter

We analyze the one-loop vacuum stability and perturbativity bounds on a singlet extension of the Standard Model (SM) scalar sector containing a scalar dark matter candidate. We show that the presence of the singlet-doublet quartic interaction relaxes the vacuum stability lower bound on the SM Higgs mass as a function of the cutoff and lowers the corresponding upper bound based on perturbativity considerations. We also find that vacuum stability requirements may place a lower bound on the singlet dark matter mass for given singlet quartic self coupling, leading to restrictions on the parameter space consistent with the observed relic density. We argue that discovery of a light singlet scalar dark matter particle could provide indirect information on the singlet quartic self-coupling.Comment: 25 pages, 10 figures; v2 - fixed minor typos; v3 - added to text discussions of other references, changed coloring of figures for easier black and white viewin