Efficient Sampling of Protein Loop Regions Using Conformational Hashing Complemented with Random Coordinate Descent

De novo construction of loop regions is an important problem in computational structural biology. Compared to regions with well-defined secondary structure, loops tend to exhibit significant conformational heterogeneity. As a result, their structures are often ambiguous when determined using experimental data obtained by crystallography, cryo-EM, or NMR. Although structurally diverse models could provide a more relevant representation of proteins in their native states, obtaining large numbers of biophysically realistic and physiologically relevant loop conformations is a resource-consuming task. To address this need, we developed a novel loop construction algorithm, Hash/RCD, that combines knowledge-based conformational hashing with random coordinate descent (RCD). This hybrid approach achieved a closure rate of 100% on a benchmark set of 195 loops in 29 proteins that range from 3 to 31 residues. More importantly, the use of templates allows Hash/RCD to maintain the accuracy of state-of-the-art coordinate descent methods while reducing sampling time from over 400 to 141 ms. These results highlight how the integration of coordinate descent with knowledge-based sampling overcomes barriers inherent to either approach in isolation. This method may facilitate the identification of native-like loop conformations using experimental data or full-atom scoring functions by allowing rapid sampling of large numbers of loops. In this manuscript, we investigate and discuss the advantages, bottlenecks, and limitations of combining conformational hashing with RCD. By providing a detailed technical description of the Hash/RCD algorithm, we hope to facilitate its implementation by other researchers.

Specificity of the chromophore-binding site in human cone opsins

The variable composition of the chromophore-binding pocket in visual receptors is essential for vision. The visual phototransduction starts with the cis-trans isomerization of the retinal chromophore upon absorption of photons. Despite sharing the common 11-cis-retinal chromophore, rod and cone photoreceptors possess distinct photochemical properties. Thus, a detailed molecular characterization of the chromophore-binding pocket of these receptors is critical to understanding the differences in the photochemistry of vision between rods and cones. Unlike for rhodopsin (Rh), the crystal structures of cone opsins remain to be determined. To obtain insights into the specific chromophore-protein interactions that govern spectral tuning in human visual pigments, here we harnessed the unique binding properties of 11-cis-6-membered-ring-retinal (11-cis-6mr-retinal) with human blue, green, and red cone opsins. To unravel the specificity of the chromophore-binding pocket of cone opsins, we applied 11-cis-6mr-retinal analog-binding analyses to human blue, green, and red cone opsins. Our results revealed that among the three cone opsins, only blue cone opsin can accommodate the 11-cis-6mr-retinal in its chromophore-binding pocket, resulting in the formation of a synthetic blue pigment (B6mr) that absorbs visible light. A combination of primary sequence alignment, molecular modeling, and mutagenesis experiments revealed the specific amino acid residue 6.48 (Tyr-262 in blue cone opsins and Trp-281 in green and red cone opsins) as a selectivity filter in human cone opsins. Altogether, the results of our study uncover the molecular basis underlying the binding selectivity of 11-cis-6mr-retinal to the cone opsins.

Crowd sourcing difficult problems in protein science. Protein Sci 2017;26:2118-2125. [PMID: 28762619 DOI: 10.1002/pro.3247]

Dedicated computing resources are expensive to develop, maintain, and administrate. Frequently, research groups require bursts of computing power, during which progress is still limited by available computing resources. One way to alleviate this bottleneck would be to use additional computing resources. Today, many computing devices remain idle most of the time. Passive volunteer computing exploits this unemployed reserve of computing power by allowing device-owners to donate computing time on their own devices. Another complementary way to alleviate bottlenecks in computing resources is to use more efficient algorithms. Engaging volunteer computing employs human intuition to help solve challenging problems for which efficient algorithms are difficult to develop or unavailable. Designing engaging volunteer computing projects is challenging but can result in high-quality solutions. Here, we highlight four examples.

Complex binding pathways determine the regeneration of mammalian green cone opsin with a locked retinal analogue

Phototransduction is initiated when the absorption of light converts the 11-cis-retinal chromophore to its all-trans configuration in both rod and cone vertebrate photoreceptors. To sustain vision, 11-cis-retinal is continuously regenerated from its all-trans conformation through a series of enzymatic steps comprising the "visual or retinoid" cycle. Abnormalities in this cycle can compromise vision because of the diminished supply of 11-cis-retinal and the accumulation of toxic, constitutively active opsin. As shown previously for rod cells, attenuation of constitutively active opsin can be achieved with the unbleachable analogue, 11-cis-6-membered ring (11-cis-6mr)-retinal, which has therapeutic effects against certain degenerative retinal diseases. However, to discern the molecular mechanisms responsible for this action, pigment regeneration with this locked retinal analogue requires delineation also in cone cells. Here, we compared the regenerative properties of rod and green cone opsins with 11-cis-6mr-retinal and demonstrated that this retinal analogue could regenerate rod pigment but not green cone pigment. Based on structural modeling suggesting that Pro-205 in green cone opsin could prevent entry and binding of 11-cis-6mr-retinal, we initially mutated this residue to Ile, the corresponding residue in rhodopsin. However, this substitution did not enable green cone opsin to regenerate with 11-cis-6mr-retinal. Interestingly, deletion of 16 N-terminal amino acids in green cone opsin partially restored the binding of 11-cis-6mr-retinal. These results and our structural modeling indicate that a more complex binding pathway determines the regeneration of mammalian green cone opsin with chromophore analogues such as 11-cis-6mr-retinal.

Hydrogen/Deuterium Exchange Mass Spectrometry of Human Green Opsin Reveals a Conserved Pro-Pro Motif in Extracellular Loop 2 of Monostable Visual G Protein-Coupled Receptors

Opsins comprise the protein component of light sensitive G protein-coupled receptors (GPCRs) in the retina of the eye that are responsible for the transduction of light into a biochemical signal. Here, we used hydrogen/deuterium (H/D) exchange coupled with mass spectrometry to map conformational changes in green cone opsin upon light activation. We then compared these findings with those reported for rhodopsin. The extent of H/D exchange in green cone opsin was greater than in rhodopsin in the dark and bleached states, suggesting a higher structural heterogeneity for green cone opsin. Further analysis revealed that green cone opsin exists as a dimer in both dark (inactive) and bleached (active) states, and that the predicted glycosylation sites at N32 and N34 are indeed glycosylated. Comparison of deuterium uptake between inactive and active states of green cone opsin also disclosed a reduced solvent accessibility of the extracellular N-terminal region and an increased accessibility of the chromophore binding site. Increased H/D exchange at the extracellular side of transmembrane helix four (TM4) combined with an analysis of sequence alignments revealed a conserved Pro-Pro motif in extracellular loop 2 (EL2) of monostable visual GPCRs. These data present new insights into the locus of chromophore release at the extracellular side of TM4 and TM5 and provide a foundation for future functional evaluation.

Structural Insights into the Drosophila melanogaster Retinol Dehydrogenase, a Member of the Short-Chain Dehydrogenase/Reductase Family

The 11-cis-retinylidene chromophore of visual pigments isomerizes upon interaction with a photon, initiating a downstream cascade of signaling events that ultimately lead to visual perception. 11-cis-Retinylidene is regenerated through enzymatic transformations collectively called the visual cycle. The first and rate-limiting enzymatic reaction within this cycle, i.e., the reduction of all-trans-retinal to all-trans-retinol, is catalyzed by retinol dehydrogenases. Here, we determined the structure of Drosophila melanogaster photoreceptor retinol dehydrogenase (PDH) isoform C that belongs to the short-chain dehydrogenase/reductase (SDR) family. This is the first reported structure of a SDR that possesses this biologically important activity. Two crystal structures of the same enzyme grown under different conditions revealed a novel conformational change of the NAD⁺ cofactor, likely representing a change during catalysis. Amide hydrogen-deuterium exchange of PDH demonstrated changes in the structure of the enzyme upon dinucleotide binding. In D. melanogaster, loss of PDH activity leads to photoreceptor degeneration that can be partially rescued by transgenic expression of human RDH12. Based on the structure of PDH, we analyzed mutations causing Leber congenital amaurosis 13 in a homology model of human RDH12 to obtain insights into the molecular basis of RDH12 disease-causing mutations.

Image registration and averaging of low laser power two-photon fluorescence images of mouse retina

Two-photon fluorescence microscopy (TPM) is now being used routinely to image live cells for extended periods deep within tissues, including the retina and other structures within the eye . However, very low laser power is a requirement to obtain TPM images of the retina safely. Unfortunately, a reduction in laser power also reduces the signal-to-noise ratio of collected images, making it difficult to visualize structural details. Here, image registration and averaging methods applied to TPM images of the eye in living animals (without the need for auxiliary hardware) demonstrate the structural information obtained with laser power down to 1 mW. Image registration provided between 1.4% and 13.0% improvement in image quality compared to averaging images without registrations when using a high-fluorescence template, and between 0.2% and 12.0% when employing the average of collected images as the template. Also, a diminishing return on image quality when more images were used to obtain the averaged image is shown. This work provides a foundation for obtaining informative TPM images with laser powers of 1 mW, compared to previous levels for imaging mice ranging between 6.3 mW [Palczewska G., Nat Med.20, 785 (2014) Sharma R., Biomed. Opt. Express4, 1285 (2013)].

BCL::MP-fold: Membrane protein structure prediction guided by EPR restraints

For many membrane proteins, the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as an alternative technique to study structure and dynamics of membrane proteins. The present study demonstrates the feasibility of membrane protein topology determination using limited EPR distance and accessibility measurements. The BCL::MP-Fold (BioChemical Library membrane protein fold) algorithm assembles secondary structure elements (SSEs) in the membrane using a Monte Carlo Metropolis (MCM) approach. Sampled models are evaluated using knowledge-based potential functions and agreement with the EPR data and a knowledge-based energy function. Twenty-nine membrane proteins of up to 696 residues are used to test the algorithm. The RMSD100 value of the most accurate model is better than 8 Å for 27, better than 6 Å for 22, and better than 4 Å for 15 of the 29 proteins, demonstrating the algorithms' ability to sample the native topology. The average enrichment could be improved from 1.3 to 2.5, showing the improved discrimination power by using EPR data.

Semi-automated discrimination of retinal pigmented epithelial cells in two-photon fluorescence images of mouse retinas

Automated image segmentation is a critical step toward achieving a quantitative evaluation of disease states with imaging techniques. Two-photon fluorescence microscopy (TPM) has been employed to visualize the retinal pigmented epithelium (RPE) and provide images indicating the health of the retina. However, segmentation of RPE cells within TPM images is difficult due to small differences in fluorescence intensity between cell borders and cell bodies. Here we present a semi-automated method for segmenting RPE cells that relies upon multiple weak features that differentiate cell borders from the remaining image. These features were scored by a search optimization procedure that built up the cell border in segments around a nucleus of interest. With six images used as a test, our method correctly identified cell borders for 69% of nuclei on average. Performance was strongly dependent upon increasing retinosome content in the RPE. TPM image analysis has the potential of providing improved early quantitative assessments of diseases affecting the RPE.

Postoperative Observation of Children after Endoscopic Type 1 Posterior Laryngeal Cleft Repair

Objectives

To report the perioperative management and surgical outcomes in a large series of pediatric patients with endoscopically repaired type 1 posterior laryngeal cleft (PLC).

Study Design

Case series with chart review.

Setting

Urban, tertiary care, free-standing pediatric hospital.

Subjects and Methods

Patients who underwent endoscopic carbon dioxide laser–assisted repair of type 1 posterior laryngeal clefts between January 2006 and December 2012. Medical records were reviewed.

Results

Fifty-four patients (34 male) underwent repair of type 1 PLC. Median age was 25.5 months (range, 2-120 months). Indications for repair included aspiration (n = 39; 72%), chronic bronchitis (n = 13; 24%), and stridor with feeds (n = 2; 4%). No children remained intubated postoperatively. Thirty-three patients (61%) stayed in overnight observation (“Obs PLC”) and 21 patients (39%) stayed in the pediatric intensive care unit (“PICU PLC”) postoperatively. Between Obs PLC and PICU PLC groups, there was no significant difference in age (mean 22 vs 30 months, respectively; P = .28). Comorbidities were similar between the groups. Symptoms improved in 41 of the 54 patients (76%). No postoperative complications were noted. Two patients required revision PLC repair. The cost of admitting a patient to a lower acuity location was estimated to be 60% less per day than cost of a PICU admission.

Conclusions

The endoscopic surgical repair of a type 1 PLC is successful and has a low morbidity and complication rate. Patients may be safely managed in an observation unit and without postoperative intubation. This approach achieved a marked cost reduction in postoperative care.

Noninvasive two-photon microscopy imaging of mouse retina and retinal pigment epithelium through the pupil of the eye

Two-photon excitation microscopy (TPM) can image retinal molecular processes in vivo. Intrinsically fluorescent retinyl esters in sub-cellular structures called retinosomes are an integral part of the visual chromophore regeneration pathway. Fluorescent condensation products of all–trans–retinal accumulate in the eye with age and are also associated with age-related macular degeneration (AMD). Here we report repetitive, dynamic imaging of these compounds in live mice, through the pupil of the eye. Leveraging advanced adaptive optics we developed a data acquisition algorithm that permitted the identification of retinosomes and condensation products in the retinal pigment epithelium (RPE) by their characteristic localization, spectral properties, and absence in genetically modified or drug-treated mice. This imaging approach has the potential to detect early molecular changes in retinoid metabolism that trigger light and AMD-induced retinal defects and to assess the effectiveness of treatments for these conditions.

Energetic analysis of the rhodopsin-G-protein complex links the α5 helix to GDP release

We present a model of interaction of G_i protein with activated rhodopsin (R*) which pin-points energetic contributions to activation and reconciles the β₂AR–G_s crystal structure with new and previously published experimental data. In silico analysis demonstrated energetic changes when the Gα C-terminal helix (α5) interacts with the R* cytoplasmic pocket, leading to displacement of the helical domain and GDP release. The model features a less dramatic domain opening than the crystal structure. The α5 helix undergoes a 63º rotation, accompanied by a 5.7Å translation, which reorganizes interfaces between α5 and α1 helices and between α5 and β6–α5. Changes in the β6–α5 loop displace αG. All of these movements lead to opening of the GDP binding pocket. The model creates a roadmap for experimental studies of receptormediated G protein activation.

RosettaEPR: rotamer library for spin label structure and dynamics

An increasingly used parameter in structural biology is the measurement of distances between spin labels bound to a protein. One limitation to these measurements is the unknown position of the spin label relative to the protein backbone. To overcome this drawback, we introduce a rotamer library of the methanethiosulfonate spin label (MTSSL) into the protein modeling program Rosetta. Spin label rotamers were derived from conformations observed in crystal structures of spin labeled T4 lysozyme and previously published molecular dynamics simulations. Rosetta’s ability to accurately recover spin label conformations and EPR measured distance distributions was evaluated against 19 experimentally determined MTSSL labeled structures of T4 lysozyme and the membrane protein LeuT and 73 distance distributions from T4 lysozyme and the membrane protein MsbA. For a site in the core of T4 lysozyme, the correct spin label conformation (Χ₁ and Χ₂) is recovered in 99.8% of trials. In surface positions 53% of the trajectories agree with crystallized conformations in Χ₁ and Χ₂. This level of recovery is on par with Rosetta performance for the 20 natural amino acids. In addition, Rosetta predicts the distance between two spin labels with a mean error of 4.4 Å. The width of the experimental distance distribution, which reflects the flexibility of the two spin labels, is predicted with a mean error of 1.3 Å. RosettaEPR makes full-atom spin label modeling available to a wide scientific community in conjunction with the powerful suite of modeling methods within Rosetta.

Pediatric obstructive sleep apnea syndrome

Pediatric obstructive sleep apnea syndrome (OSAS) is a common health problem diagnosed and managed by various medical specialists, including family practice physicians, pediatricians, pulmonologists, and general and pediatric otolaryngologists. If left untreated, the sequelae can be severe. Over the last decade, significant advancements have been made in the evidence-based management of pediatric OSAS. This article focuses on the current understanding of this disease, its management, and related clinical practice guidelines.

Treatment strategies for lateral sphenoid sinus recess cerebrospinal fluid leaks

OBJECTIVE

To highlight concepts critical to achieving successful repair and avoiding intracranial complications in the treatment of cerebrospinal fluid (CSF) leaks from the lateral recess of the sphenoid sinus (LRS).

DESIGN

Outcomes study.

SETTING

Tertiary referral university hospital.

PATIENTS

Eleven patients with LRS CSF leaks from June 2008 to June 2010.

INTERVENTIONS

Endoscopic transpterygoid approach and multilayer repair of skull base defect in the LRS.

MAIN OUTCOME MEASURES

Recurrence, graft techniques, postoperative intracranial pressure (ICP), and use of ventriculoperitoneal (VP) shunt.

RESULTS

Thirteen CSF leaks originating in the LRS were surgically repaired in 11 patients; 2 patients required bilateral leak repair. The endoscopic transpterygoid approach was used in 12 of 13 repairs. Eight patients had failed attempts at repair prior to presentation (4 endoscopic sphenoidotomies and 4 middle cranial fossa [MCF] approaches). One patient presented with a temporal lobe abscess following hydroxyapatite "obliteration" to seal off the LRS. This required a combined MCF/transpterygoid approach to drain the abscess, remove the encephalocele and hydroxyapatite, and seal the skull base defect. In 2 cases, the LRS was left patent owing to concerns of inadequate mucosal extirpation. The median duration of follow-up was 10.8 months (range, 2-29 months). One patient experienced a failure (2 months after repair), which was successfully sealed on the second attempt. Postoperatively, 5 patients required VP shunts, and 5 were maintained on acetazolamide for elevated ICP (average, 26.7 cm H₂O in 8 patients; presumed elevated in 2 patients).

CONCLUSIONS

The current study demonstrated a 92% success rate using the endoscopic transpterygoid approach for LRS skull base defects providing support for routine use in the treatment algorithm. Poor outcomes were observed with previous surgical attempts to obstruct the LRS without repairing the skull base defect.

Cystic fibrosis transmembrane conductance regulator modulation by the tobacco smoke toxin acrolein

OBJECTIVES/HYPOTHESIS

Evidence indicates that decreased mucociliary clearance (MCC) is a major contributing feature to chronic rhinosinusitis. Tobacco-smoke exposure is thought to inhibit transepithelial Cl(-) secretion, a major determinant of airway surface liquid hydration and MCC. The objective of the current study was to evaluate the effects of acrolein exposure (a prominent tobacco smoke toxin) on vectorial Cl(-) transport through the major apical anion channel cystic fibrosis transmembrane conductance regulator (CFTR) in sinonasal epithelium.

STUDY DESIGN

In vitro investigation.

METHODS

Primary murine nasal septal epithelia (MNSE; wild-type and transgenic CFTR(-/-)) cultures were exposed to acrolein in Ussing chambers and the effects on Cl(-) secretion investigated using pharmacologic manipulation. Cellular cyclic adenosine monophosphate (cAMP) signaling and cytotoxicity were also investigated.

RESULTS

Acrolein stimulated Cl(-) secretion (ΔI(SC) - change in short-circuit current in μA/cm(2)) at concentrations similar to smoker's airways (100 μM, 15.8 ± 2.2 vs. 2.4 ± 0.8 [control]; P < .0001), suppressed forskolin-stimulated C- transport at 300 μM (13.3 ± 1.2 vs. 19.9 ± 1.0; P < .01), and completely abolished all transport at 500 μM (-1.1 ± 1.6). Stimulated Cl(-) secretion was solely reliant upon the presence of CFTR (confirmed in transgenic CFTR(-/-) MNSE), but independent of cAMP signaling. Inhibition at higher concentrations was not secondary to cellular cytotoxicity.

CONCLUSIONS

The present study demonstrates that acrolein has complex but pronounced interaction with the major apical Cl(-) transport mechanism that uses CFTR. Further investigations are required to determine acrolein's impact as a tobacco smoke constituent on mucociliary transport.

CFTR Modulation by the Tobacco Smoke Toxin Acrolein

Objective: Tobacco-smoke exposure inhibits transepithelial Cl-secretion—a major determinant of airway surface liquid hydration and mucociliary clearance (MCC). The objective of the current study was to evaluate the effects of acrolein exposure (a tobacco smoke toxin) on Cl-transport through the major apical anion channel CFTR in sinonasal epithelium.

Method: Primary murine nasal septal (MNSE, wild type, and transgenic CFTR-/-) and human sinonasal epithelial (HSNE) cultures were exposed to acrolein in Ussing chambers, and effects on Cl-secretion were investigated using pharmacologic manipulation. Cellular cAMP signaling and cytotoxicity were also investigated.

Results: Acrolein-stimulated Cl-secretion (ΔISC - change in short-circuit current in µA/cm2) at low concentrations (100 µM, 15.8 ± 2.2 vs 2.4 ± 0.8 (control); p-transport at 300 µM (13.3 ± 1.2 vs 19.9 ± 1.0; p-secretion was solely reliant upon the presence of CFTR (confirmed in transgenic CFTR -/- MNSE), but independent of cAMP signaling. Inhibition at higher concentrations was not secondary to cellular cytotoxicity, indicating direct effects on the CFTR.

Conclusion: Decreased MCC is a major contributing feature to chronic rhinosinusitis. The present study demonstrated that acrolein has complex but direct interactions with CFTR. Robust inhibition of Cl-transport at higher concentrations indicates the potential contribution of this toxin to decreased MCC in individuals with chronic tobacco smoke exposure.

Resveratrol has salutary effects on mucociliary transport and inflammation in sinonasal epithelium

OBJECTIVE/HYPOTHESIS

Therapeutic agents that enhance mucociliary transport (via stimulation of transepithelial Cl- secretion) and inhibit inflammation could provide considerable advantages over conventional treatments for chronic rhinosinusitis (CRS). The objectives of the present study were to investigate whether the polyphenolic compound resveratrol promotes transepithelial Cl- transport and inhibits KC/IL-8 secretion in sinonasal epithelium.

STUDY DESIGN

In vitro and in vivo study.

METHODS

Transepithelial Cl- transport was investigated in primary murine nasal septal (MNSE) and human sinonasal epithelial (HSNE) cultures. In vivo activity was also measured using the murine nasal potential difference assay. CFTR R-domain phosphorylation and cAMP levels were examined as a test of cAMP/PKA-dependent activation. In vitro LPS-induced KC/IL-8 secretion was quantified and compared to a panel of intranasal steroids.

RESULTS

Resveratrol(100 μM) significantly increased CFTR-mediated Cl- transport (change in short-circuit current, ΔI(SC) ) in both MNSE (13.51 ± 0.77 vs. 4.4 ± 0.66 [control]; P < .05) and HSNE (12.28 ± 1.08 vs. 0.69 ± 0.32 [control]; P < .05). Cl- secretion across in vivo murine nasal epithelium was also enhanced (-4 ± 1.8 vs. -0.8 ± 1.7mV [control], P < .05). There was no increase in cellular cAMP or CFTR R-domain phosphorylation detected. Resveratrol also significantly inhibited KC/IL-8 secretion in a dose-dependent fashion (pg/mL) in MNSE (181 ± 39[100 μM) vs. 94 ± 16 [200 μM] vs. 16 ± 22 [500 μM] vs. 1195 ± 355 [LPS control]; P < .001). The compound robustly abrogated KC/IL-8 secretion when compared to ciclesonide (765 ± 139), triamcinolone (561 ± 124), and budesonide (742 ± 428), but had similar activity to fluticasone proprionate (65 ± 47). Similar effects were demonstrated in HSNE (975 ± 244 [100 μM] vs. 1825 ± 144 [LPS control]; P < .001) with inhibition comparable to fluticasone proprionate (785 ± 277).

CONCLUSIONS

These in vitro and in vivo findings indicate resveratrol is a potent Cl- secretagogue and anti-inflammatory agent. Future clinical trials for CRS are warranted.

Fixation Methods in Pediatric Cochlear Implants

Objective. To review 3 techniques of cochlear implant (CI) fixation used by a single surgeon for the fixation of 320 consecutive CIs in a pediatric population and associated complications.

Study Design. Case series with chart review.

Setting. Tertiary referral children’s hospital.

Subjects and Methods. Patients receiving CIs between July 1995 and July 2009 were reviewed. Clinical information obtained included age at implant, implant type, duration of follow-up, method of implant fixation (intraosseous suture ligature, prolene mesh with titanium screws, and a small periosteal pocket with periosteal sutures), and postoperative complications of fixation (migration or extrusion).

Results. Three hundred twenty consecutive CIs were reviewed: 64 of which were bilateral (42 staged, 22 concurrent). The median age at implantation was 3.6 years (range, 8 months to 20 years). Manufacturers included Cochlear (223) and Advanced Bionics Corporation (97). Median follow-up was 26 months (range, 1 month to 12.7 years). The intraosseous suture ligation method of fixation was used for 182 CIs. Ninety-eight CIs were fixed using a small piece of polypropylene mesh and titanium screws. Forty implants were secured by using a tight periosteal pocket and placing the suture through the periosteum and soft tissue to collar the receiver in a modified well. No complications of device migration or extrusion were noted, nor were there any intracranial complications. Device failure occurred in 13 (4%) patients requiring explantation and reimplantation, but these were unrelated to surgical technique or fixation.

Conclusions. This study illustrates that with an evolution toward less invasive and less complex methods of fixation, there has not been an associated increase in fixation-related complications.

Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination

A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al. (2008)). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure elements yielded vastly improved models by Rosetta folding. 54% of all these models have the correct fold compared to only 21% and 8% correctly folded models when randomly placed restraints or no restraints are used, respectively. Moreover, the improvements in model quality require a limited number of optimized restraints, which is determined by the pairwise connectivities of T4L α-helices. The predicted improvement in Rosetta model quality was verified by experimental determination of distances between spin labels pairs selected by the algorithm. Overall, our results reinforce the rationale for the combined use of sparse EPR distance restraints and de novo folding. By alleviating the experimental bottleneck associated with restraint selection, this algorithm sets the stage for extending computational structure determination to larger, traditionally elusive protein topologies of critical structural and biochemical importance.

Transduction of multiple cell types using improved conditions for gene delivery and expression of SV40 pseudovirions packaged in vitro

This comprehensive study demonstrates highly efficient transduction of a wide variety of human, murine, and monkey cell lines, using a procedure for in vitro packaging of plasmid DNA in recombinant simian virus 40 (SV40) capsid proteins to form pseudovirions. The pseudovirions are encapsidated by the VP1 major capsid protein, with no SV40 sequence requirement, and are able to carry up to 17.7 kb of supercoiled plasmid DNA. We developed a procedure to scale-up production of SV40 pseudovirions, as well as an efficient protocol to concentrate the virions with no loss of activity. We also developed a method that allows transduction of 10 times more cells than the original protocol. This protocol was tested using supercoiled in vitro-packaged plasmid carrying the human multidrug-resistance gene (MDR1 encoding P-glycoprotein; P-gp), or the enhanced green fluorescent protein reporter gene (EGFP) in .45 human lymphoblastoid cells and in K562 human erythroleukemia cells. Multiple transductions at 24-h intervals were shown to increase expression using the EGFP reporter gene. The protocols developed in this study establish in vitro-packaged SV40 pseudovirions as one of the most efficient gene delivery systems.

Prevention of wound infections. A case for closed suction drainage to remove wound fluids deficient in opsonic proteins

Fluids collecting in surgical wounds in both dogs and man have been shown to lose progressively the ability to opsonize bacteria for phagocytosis and killing of bacteria by normal neutrophils. Since the collection of fluids in potentially contaminated wounds also interferes with access of phagocytic cells to contaminating bacteria and provides a pablum for growth, their removal seems to be indicated to minimize the risk of infection. This can be accomplished easily and safely with the use of closed suction drainage as demonstrated in 100 patients undergoing bilateral nephrectomy, splenectomy, and renal transplantation.

The influence of route of administration on wound fluid concentration of prophylactic antibiotics

The effectiveness of prophylactic antibiotics is dependent upon both the antimicrobial potency of the drug and the time at which it is first administered. Effectiveness is progressively lost when therapy is delayed, and it is generally recognized that drugs administered only 3-4 hours after contamination of a wound are largely without benefit. Another factor potentially influencing effectiveness in the traumatized patient is the considerable variation in the rate in which various antibiotics penetrate into the interstitial fluid compartment of surgical or traumatic wounds. The present study investigated the effect of route and method of administration of ampicillin, gentamicin, clindamycin, tetracycline, and cephalothin on subsequent wound fluid concentrations. Equivalent doses of each antibiotic were administered by either intermittent intravenous bolus (IV Push), continuous IV infusion (IV Cont) or intermittent intramuscular injection (IM). Peripheral blood and wound tissue fluid from previously implanted stainless steel cylinders were sampled sequentially during an 18 to 24 hour period and assayed for concentration of the antibiotic. Each antibiotic had a different pattern of distribution between serum and wound tissue compartments, but in general, the IV Push method showed comparable levels in wound fluid 4-12 times faster than the IV Cont method. After 12 hours, the highest sustained antibiotic concentrations in wound fluid was usually achieved with the IM route. These data suggest that the earliest and most sustained levels of antibiotic in wound tissue fluid can be achieved by a simultaneous IV Push and IM injection of the drug followed by intermittent IM injections in the normotensive patient or by an IV Push followed by IV Cont administration for patients in shock. These techniques are recommended when it is not possible to administer prophylactic antibiotics before bacterial contamination has occurred, such as regularly occurs in the traumatized patient, especially when treatment is delayed.