An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations.

An implementation of the replica exchange with dynamical scaling (REDS) method in the commonly used molecular dynamics program GROMACS is presented. REDS is a replica exchange method that requires fewer replicas than conventional replica exchange while still providing data over a range of temperatures and can be used in either constant volume or constant pressure ensembles. Details for running REDS simulations are given, and an application to the human islet amyloid polypeptide (hIAPP) 11-25 fragment shows that the model efficiently samples conformational space.

In silico modeling of the cryptic E2∼ubiquitin-binding site of E6-associated protein (E6AP)/UBE3A reveals the mechanism of polyubiquitin chain assembly.

To understand the mechanism for assembly of Lys48-linked polyubiquitin degradation signals, we previously demonstrated that the E6AP/UBE3A ligase harbors two functionally distinct E2∼ubiquitin-binding sites: a high-affinity Site 1 required for E6AP Cys820∼ubiquitin thioester formation and a canonical Site 2 responsible for subsequent chain elongation. Ordered binding to Sites 1 and 2 is here revealed by observation of UbcH7∼ubiquitin-dependent substrate inhibition of chain formation at micromolar concentrations. To understand substrate inhibition, we exploited the PatchDock algorithm to model in silico UbcH7∼ubiquitin bound to Site 1, validated by chain assembly kinetics of selected point mutants. The predicted structure buries an extensive solvent-excluded surface bringing the UbcH7∼ubiquitin thioester bond within 6 Šof the Cys820 nucleophile. Modeling onto the active E6AP trimer suggests that substrate inhibition arises from steric hindrance between Sites 1 and 2 of adjacent subunits. Confirmation that Sites 1 and 2 function in trans was demonstrated by examining the effect of E6APC820A on wild-type activity and single-turnover pulse-chase kinetics. A cyclic proximal indexation model proposes that Sites 1 and 2 function in tandem to assemble thioester-linked polyubiquitin chains from the proximal end attached to Cys820 before stochastic en bloc transfer to the target protein. Non-reducing SDS-PAGE confirms assembly of the predicted Cys820-linked 125I-polyubiquitin thioester intermediate. Other studies suggest that Glu550 serves as a general base to generate the Cys820 thiolate within the low dielectric binding interface and Arg506 functions to orient Glu550 and to stabilize the incipient anionic transition state during thioester exchange.

Facet-sparing decompression with a minimally invasive flexible microblade shaver: a prospective operative analysis.

STUDY DESIGN: This is a detailed description of a facet-sparing decompression technique and a prospective observational study of 59 subjects. OBJECTIVE: To describe a facet-sparing decompression technique, quantify operative parameters, adverse events, and anatomic changes following decompression with a flexible microblade shaving system. SUMMARY OF BACKGROUND DATA: Decompression in patients with lumbar spinal stenosis is a common surgical procedure. However, obtaining a thorough decompression while leaving enough tissue to avoid destabilization can be challenging. Decompression with a flexible, through-the-foramen system may mitigate some of these challenges. MATERIALS AND METHODS: Fifty-nine subjects diagnosed with lumbar spinal stenosis were recruited into this study. Subjects underwent decompression with a flexible, microblade decompression system at a total of 88 levels between L2 and S1. Subject demographics, details of the procedure, and operation, including adverse events were collected. Preoperative and postoperative computed tomography scans and plain radiographs were obtained from a subset of 12 subjects and quantitatively assessed for bone removal and preservation of stabilizing structures. RESULTS: Fifty-nine subjects had 88 levels treated, 51% single-level and 49% 2-level with L4-L5 being the most commonly decompressed level. Operative time, blood loss, and length of stay were similar to or less than that seen in the historical control. The system was successfully used for decompression in 95.8% of the attempted foramina. Three operative complications were reported, all dural tears (5.1%). These dural tears occurred before introduction of the flexible decompression system. Computed tomography scans from 12 subjects demonstrate access to the lateral recess and foramen with removal of <6% of the superior facet cross-sectional area. CONCLUSIONS: The flexible microblade shaving system provided thorough decompression with few intraoperative complications. Operative variables were favorable compared to the literature and radiographic decompression was achieved to a great extent while allowing for the preservation of the facet joints and midline structures.

Facet-sparing lumbar decompression with a minimally invasive flexible MicroBlade Shaver® versus traditional decompression: quantitative radiographic assessment.

BACKGROUND: Laminectomy/laminotomy and foraminotomy are well established surgical techniques for treatment of symptomatic lumbar spinal stenosis. However, these procedures have significant limitations, including limited access to lateral and foraminal compression and postoperative instability. The purpose of this cadaver study was to compare bone, ligament, and soft tissue morphology following lumbar decompression using a minimally invasive MicroBlade Shaver® instrument versus hemilaminotomy with foraminotomy (HL). METHODS: The iO-Flex® system utilizes a flexible over-the-wire MicroBlade Shaver instrument designed for facet-sparing, minimally invasive "inside-out" decompression of the lumbar spine. Unilateral decompression was performed at 36 levels in nine human cadaver specimens, six with age-appropriate degenerative changes and three with radiographically confirmed multilevel stenosis. The iO-Flex system was utilized on alternating sides from L2/3 to L5/S1, and HL was performed on the opposite side at each level by the same investigator. Spinal canal, facet joint, lateral recess, and foraminal morphology were assessed using computed tomography. RESULTS: Similar increases in soft tissue canal area and decreases in ligamentum flavum area were noted in nondiseased specimens, although HL required removal of 83% more laminar area (P < 0.01) and 95% more bone resection, including the pars interarticularis and facet joints (P < 0.001), compared with the iO-Flex system. Similar increases in lateral recess diameter were noted in nondiseased specimens using each procedure. In stenotic specimens, the increase in lateral recess diameter was significantly (P = 0.02) greater following use of the iO-Flex system (43%) versus HL (7%). The iO-Flex system resulted in greater facet joint preservation in nondiseased and stenotic specimens. In stenotic specimens, the iO-Flex system resulted in a significantly greater increase in foraminal width compared with HL (24% versus 4%, P = 0.01), with facet joint preservation. CONCLUSION: The iO-Flex system resulted in significantly better decompression of the lateral recess and foraminal areas compared with HL, while preserving posterior spinal elements, including the facet joint.

Crosstalk between PKA and Epac regulates the phenotypic maturation and function of human dendritic cells.

The cAMP-dependent signaling pathways that orchestrate dendritic cell (DC) maturation remain to be defined in detail. Although cAMP was previously thought to signal exclusively through protein kinase A (PKA), it is now clear that cAMP also activates exchange protein activated by cAMP (Epac), a second major cAMP effector. Whether cAMP signaling via PKA is sufficient to drive DC maturation or whether Epac plays a role has not been examined. In this study, we used cAMP analogs to selectively activate PKA or Epac in human monocyte-derived DCs and examined the effect of these signaling pathways on several hallmarks of DC maturation. We show that PKA activation induces DC maturation as evidenced by the increased cell-surface expression of MHC class II, costimulatory molecules, and the maturation marker CD83. PKA activation also reduces DC endocytosis and stimulates chemotaxis to the lymph node-associated chemokines CXCL12 and CCL21. Although PKA signaling largely suppresses cytokine production, the net effect of PKA activation translates to enhanced DC activation of allogeneic T cells. In contrast to the stimulatory effects of PKA, Epac signaling has no effect on DC maturation or function. Rather, Epac suppresses the effects of PKA when both pathways are activated simultaneously. These data reveal a previously unrecognized crosstalk between the PKA and Epac signaling pathways in DCs and raise the possibility that therapeutics targeting PKA may generate immunogenic DCs, whereas those that activate Epac may produce tolerogenic DCs capable of attenuating allergic or autoimmune disease.

Computational de novo design, and characterization of an A(2)B(2) diiron protein.

Diiron proteins are found throughout nature and have a diverse range of functions; proteins in this class include methane monooxygenase, ribonucleotide reductase, Delta(9)-acyl carrier protein desaturase, rubrerythrin, hemerythrin, and the ferritins. Although each of these proteins has a very different overall fold, in every case the diiron active site is situated within a four-helix bundle. Additionally, nearly all of these proteins have a conserved Glu-Xxx-Xxx-His motif on two of the four helices with the Glu and His residues ligating the iron atoms. Intriguingly, subtle differences in the active site can result in a wide variety of functions. To probe the structural basis for this diversity, we designed an A(2)B(2) heterotetrameric four-helix bundle with an active site similar to those found in the naturally occurring diiron proteins. A novel computational approach was developed for the design, which considers the energy of not only the desired fold but also alternatively folded structures. Circular dichroism spectroscopy, analytical ultracentrifugation, and thermal unfolding studies indicate that the A and B peptides specifically associate to form an A(2)B(2) heterotetramer. Further, the protein binds Zn(II) and Co(II) in the expected manner and shows ferroxidase activity under single turnover conditions.