A Preclinical Cadaver Fitting Study of Implantable Biventricular Assist Device - AnyHeart™

A multifunctional, Korean-made artificial heart (AnyHeart™) was developed, and prior to its clinical application, a cadaver-fitting study was performed. The study proposed to determine the optimal cannulation approach, implantation technique and route of the cannula to minimize the organ compression of AnyHeart™. The anatomical feasibility and a variety of surgical techniques were evaluated using ten preserved, human cadavers. Implanting AnyHeart™ with ease is possible using various approaches, including a median sternotomy, and a right or left lateral thoracotomy. The lateral thoracotomy approach is shown to be safe and reproducible, especially in patients who have already undergone an operation that used a median sternotomy. The results of this study will guide improvements in the designs of cannulae and AnyHeart™ for future clinical applications.

Characterization of the AWARE 10 two-gigapixel wide-field-of-view visible imager

System requirements for many military electro-optic and IR camera systems reflect the need for both wide-field-of-view situational awareness as well as high-resolution imaging for target identification. In this work we present a new imaging system architecture designed to perform both functions simultaneously and the AWARE 10 camera as an example at visible wavelengths. We first describe the basic system architecture and user interface followed by a laboratory characterization of the system optical performance. We then describe a field experiment in which the camera was used to identify several maritime targets at varying range. The experimental results indicate that users of the system are able to correctly identify ~10 m targets at between 4 and 6 km with 70% accuracy.

Comparison of cystatin C- and creatinine-based estimation of glomerular filtration rate according to glycaemic status in Type 2 diabetes

AIMS

The influence of hyperglycaemia on the performance of glomerular filtration rate (GFR) estimating equations remains to be determined. We compared the performance of creatinine-based GFR with cystatin C-based GFR in patients with Type 2 diabetes according to glycaemic status.

METHODS

In a cross-sectional study of 210 patients with Type 2 diabetes, we staged glycaemic status by HbA(1c) tertiles [HbA(1c) ≤ 75 mmol/mol (9.0%) (n = 70), HbA(1c) 76-95 mmol/mol (9.1-10.8%) (n = 70), HbA(1c) >95 mmol/mol (10.8%) (n = 70)] and measured GFR. Isotopic GFR was measured using renal dynamic imaging with (99m) Tc-diethylene-triamine-penta-acetic acid. Estimated GFR (eGFR) was measured using creatinine-based formulae (Cockcroft-Gault-eGFR, the Modification of Diet in Renal Disease equation-eGFR and the Chronic Kidney Disease Epidemiology Collaboration formula-eGFR) and a cystatin C-based formula (cystatin C-eGFR).

RESULTS

The isotopic GFR of all patients was 93.1 ± 34.1 ml min(-1) 1.73 m(-2). All methods for estimating GFR underestimated isotopic GFR [Cockcroft-Gault-eGFR (68.8 ± 38.6 ml min(-1) 1.73 m(-2) ) (P < 0.05), Modification of Diet in Renal Disease-eGFR (74.8 ± 31.3 ml min(-1) 1.73 m(-2) ) (P < 0.05), Chronic Kidney Disease Epidemiology Collaboration-eGFR (72.9 ± 26.6 ml min(-1) 1.73 m(-2)) (P < 0.05) and cystatin C-eGFR (83.5 ± 33.2 ml min(-1) 1.73 m(-2)) (P < 0.05)]. In all patient groups, cystatin C-eGFR was less biased and more accurate than the creatinine-based formulae, especially in the group with HbA(1c) > 95 mmol/mol (10.8%) where there was no difference between cystatin C-eGFR and isotopic GFR.

CONCLUSIONS

Performance of cystatin C-eGFR was superior to creatinine-based GFR in patients with Type 2 diabetes with HbA(1c) >95 mmol/mol (10.8%).

Oncologic outcome after cessation or dose reduction of capecitabine in patients with colon cancer

Purpose

Oral capecitabine has been used as adjuvant therapy for colorectal cancer patients since the 1990s. Patient-initiated cessation or reduced use of capecitabine occurs widely for various reasons, yet the consequences of these actions are unclear. The present study sought to clarify treatment outcomes in such patients.

Methods

The study included 173 patients who had been diagnosed with stage II or III colon cancer according to the pathologic report after radical surgery at Samsung Medical Center from May 2005 to June 2007 and who had received capecitabine as adjuvant therapy. The patients were divided into groups according to whether the dose was reduced (I, dose maintenance; II, dose reduction) or stopped (A, cycle completion; B, cycle cessation). Recurrence and disease-free survival rates between the two groups each were analyzed.

Results

Of the 173 patients, 128 (74.6%) experienced complications, most frequently hand-foot syndrome (n = 114). Reduction (n = 35) or cessation (n = 18) of medication was most commonly due to complications. Concerning reduced dosage, both groups displayed no statistically significant differences in recurrence rate and 3-year disease-free survival rate. Concerning discontinued medication use, the cycle completion group showed an improved recurrence rate (P = 0.048) and 3-year disease-free survival rate (P = 0.028).

Conclusion

The results demonstrate that maintaining compliance with capecitabine as an adjuvant treatment for colon cancer to preventing complications positively affects patient prognosis.

The relationship between adipokines, metabolic parameters and insulin resistance in patients with metabolic syndrome and type 2 diabetes

This study was designed to investigate the relationship between adipokines in metabolic syndrome and insulin resistance. Sixty male and female subjects with or without metabolic syndrome and type 2 diabetes were included. The homeostasis model assessment of insulin resistance (HOMA-IR) was calculated. Compared with lean control subjects, patients with metabolic syndrome and type 2 diabetes had lower circulating levels of total adiponectin and high molecular weight (HMW) adiponectin, and higher levels of leptin and interleukin-6 (IL-6). Total and HMW adiponectin and the adiponectin/leptin (A/L) ratio were negatively correlated with HOMA-IR. After adjusting for age and sex, leptin, IL-6 and tumour necrosis factor-alpha (TNF-alpha) were positively correlated with HOMA-IR. After also adjusting for body mass index, HOMA-IR was found to be independently associated with leptin, A/L ratio and TNF-alpha levels. In conclusion, decreased total adiponectin and HMW adiponectin and increased leptin and IL-6 levels are characteristic of patients with metabolic syndrome and type 2 diabetes.

Compliance and effective management of the hand-foot syndrome in colon cancer patients receiving capecitabine as adjuvant chemotherapy

PURPOSE

Physicians and oncology nurses must continue to update their knowledge on treatment and treatment-related side effects, while searching for effective methods to prevent or manage side effects. The objective of our study was to describe the incidence and response to treatment of the hand-foot syndrome (HFS) and the compliance with treatment of patients with stage IIB, IIIA, IIIB, and IIIC colon cancer that were treated with capecitabine alone as adjuvant therapy.

MATERIALS AND METHODS

Between September 2005 and September 2006, 84 patients fulfilled the inclusion criteria and were included in this retrospective analysis of prospectively collected data.

RESULTS

The treatment compliance rate was 90.5% (76 out of the 84 patients). The HFS developed in 65 patients (77.4%). Thirty-three patients (50.7%) had grade 1 HFS, 22 patients (33.8%) had grade 2 HFS and 10 patients (15.5%) had grade 3 HFS, as their most severe episode. For Grade 1 patients, the dose was maintained, and skin barrier cream and moist exposed burn ointment (MEBO) were applied. For Grade 2 patients, either the dose was maintained or 25% of the dose was reduced; MEBO and supportive care were provided. For Grade 3 patients, one cycle of chemotherapy was interrupted followed by dose adjustment; MEBO and supportive care were provided.

CONCLUSION

HFS is manageable if both patients and oncology care teams are educated about HFS associated with capecitabine. The HFS is treated by patient education, preventive management, ointment application, conservative management, dose reduction, and interruption of chemotherapy administration.

Recent progress of moving-actuator type mechanical circulatory support systems: AnyHeart and T-PLS

The mechanical circulatory support system using moving-actuator mechanisms were developed by Seoul National University and Korea University. AnyHeart is a fully implanted pulsatile bi-ventricular assist device, and T-PLS is a pulsatile flow versatile extracorporeal life support system. Through lots of in-vitro and in-vivo experiments, the developed mechanical systems are faced to produce on commercial scale. This paper describes the recent progress of two mechanical circulatory support systems, AnyHeart and T-PLS.

Effects of ultraviolet intensity and wavelength on the photolysis of triclosan

The effects of ultraviolet (UV) intensity and wavelength on triclosan (TCS) photodegradation kinetic, efficiency, mechanisms and pathway were studied. The TCS photodegradation followed the pseudo-first order kinetic model at all UV intensities examined at the wavelengths of 254 and 365 nm and the photodegradation rate increased with increasing UV intensity. TCS photodegradation efficiencies of 90 to 98% and 79 to 90% were obtained at the wavelengths of 254 and 365 nm, respectively. TCS was degraded mainly by photon induced hydroxyl radicals while the direct photon reaction with TCS played a subordinate role. Chlorophenol, dichlorophenol and phenol were the intermediates detected in all experiments conducted. Dibenzodichloro-p-dioxin and dibenzo-p-dioxin were observed as the intermediates only at lower UV intensities investigated at the wavelength of 365 nm. Based on these intermediates, a complete TCS photolysis pathway was proposed for the first time.

Degradation kinetics and mechanism of RDX and HMX in TiO2 photocatalysis

This study was undertaken to examine the photocatalytic degradation of explosives hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) with a circular photocatalytic reactor, using a UV lamp as a light source and TiO2 as a photocatalyst. The effects of various parameters, such as the RDX or HMX concentration, the amount of TiO, and the initial pH, on the photocatalytic degradation rates of explosives were examined. In the presence of both UV light and TiO2 RDX and HMX were more effectively degraded than with either UV or TiO2 alone. The degradation rates were found to obey pseudo-first-order kinetics represented by the Langmuir-Hinshelwood model. Increases in the RDX and HMX degradation rates were obtained with decreasing initial concentrations of the explosives. The RDX and HMX degradation rates were higher at pH 7 than at either pH 3 or pH 11. A dose of approximately 0.7 g l(-1) of TiO2 degraded HMX more rapidly than did higher or lower TiO2 doses. RDX (20 mg l(-1)) photocatalysis resulted in an approximately 20% decrease in TOC, and HMX (5 mg l(-1)) photocatalysis resulted in a 60%, decrease in TOC within 150 minutes. A trace amount of formate was produced as an intermediate that was further mineralized by RDX or HMX photocatalysis. The nitrogen byproducts from the photocatalysis of RDX and HMX were mainly NO3- with NO2-, and NH4+. The total nitrogen recovery was about 60% from RDX (20 mg l(-1)), and 70% from HMX (5 mg l(-1)), respectively. Finally, a mechanism for RDX/HMX photocatalysis was proposed, along with supporting qualitative and quantitative evidence.

The effects of pulsatile versus non-pulsatile extracorporeal circulation on the pattern of coronary artery blood flow during cardiac arrest

BACKGROUND

In sudden cardiac arrest, the effective maintenance of coronary artery blood flow is of paramount importance for myocardial preservation as well as cardiac recovery and patient survival. The purpose of this study was to directly compare the effects of pulsatile versus non-pulsatile circulation to coronary artery flow and myocardial preservation in a cardiac arrest condition.

METHODS

A cardiopulmonary bypass circuit was constructed in a ventricular fibrillation model using fourteen Yorkshire swine weighing 25-35 kg each. The animals were randomly assigned to group I (n=7, non-pulsatile centrifugal pump) or group II (n=7, pulsatile T-PLS pump). Extracorporeal circulation was maintained for two hours at a pump flow of 2 L/min. The left anterior descending coronary artery flow was measured with an ultrasonic coronary artery flow measurement system at baseline (before bypass) and at every 20 minutes after bypass. Serologic parameters were collected simultaneously at baseline, 1 hour, and 2 hours after bypass in the systemic arterial and coronary sinus venous blood. The Mann-Whitney U test of STATISTICA 6.0 was used to determine intergroup significances using a p value of <0.05.

RESULTS

The resistance index of the coronary artery was lower in group II and the difference was significant at 40 min, 80 min, 100 min and 120 min (p<0.05). The mean velocity of the coronary artery was higher in group II throughout the study, and the difference was significant from 20 min after starting the pump (p<0.05). The coronary artery blood flow was higher in group II throughout the study, and the difference was significant from 40 min to 120 min (p<0.05) except at 80 min. Serologic parameters showed no differences between the groups at 1 hour and 2 hours after bypass in the systemic and coronary sinus blood (p=NS).

CONCLUSION

In the cardiac arrest condition, pulsatile extracorporeal circulation provides more blood flow, higher flow velocity and less resistance to coronary artery than non-pulsatile circulation.

Robust Motor Speed Control under Time Varying Loads in Moving Actuator Type artificial Heart (AnyHeart)

The Moving Actuator type artificial heart(AnyHeart) as well as many other artificial hearts uses a motor as its power source. For controllability of control parameters such as pump rate, pump output, blood pressure profile and flow form, the precise motor speed control is important. However, because the implantable device has limited carrying capacity of hardware components in size and number, applying diverse motor control methods are not possible. In addition, the existing PI (Proportional-Integral) motor controller does not show satisfactory performance.

A new controller that is sufficiently robust for the changes of load and physical system parameters has been designed and tested. The robust speed controller is based on the sliding mode control method that is applicable to a system of which the ranges of uncertainty in physical parameters are known.

In a mock circulation system test, the actual speed showed good tracking characteristics in respect to the reference speed. Fast follow-up characteristics were also observed under high afterload and speed conditions. The speed error, current and power consumption were reduced by about 40%. The proposed control technique overcomes the limitations of the PI controller, and makes important improvements in both performance and stability.

Expression of the intermediate filament vimentin in proliferating duct cells as a marker of pancreatic precursor cells

OBJECTIVES

The expression of the intermediate filament (IF) vimentin, usually considered a marker of mesenchymal cells, has been observed in the epithelial cells during embryogenesis, carcinogenesis, and dedifferentiation, suggesting that it might be useful as a marker of proliferating precursor cells in the pancreas.

METHODS

Rat pancreata at E18 and at different time points after partial pancreatectomy (Px) and human and neonatal pig pancreatic tissue sections and monolayer cultured pancreatic duct cells were observed. All tissues were simultaneously immunostained with pancytokeratin and vimentin antibodies. In costained duct cells, PDX-1 or PCNA expression was also analyzed using confocal microscope images.

RESULTS

In the rat embryonic pancreas at E18, all epithelial cells that formed ductlike structures expressed both cytokeratin and vimentin IF, whereas no duct cells costained for IF in the adult rat or neonatal pig pancreas. Such costaining reappeared in the following order: common pancreatic duct, main ducts, foci of regeneration and then disappeared completely at 30 days after Px. In humans, costaining was found in only 1 diabetic patient's pancreatic section, which was accompanied by massive duct cell proliferation. In monolayer culture, most of the duct cells of human and neonatal pigs coexpressed both IF proteins. Only a few costained duct cells also expressed PDX-1, and most of those cells were also stained with PCNA in rat embryonic pancreas and regenerating foci after partial Px.

CONCLUSIONS

Vimentin IF expression might be a useful marker for pancreatic precursor cells and could be used to investigate the concept of the dedifferentiation of fully matured duct cells during the process of the beta-cell neogenesis.

Applications of the pulsatile flow versatile ECLS: in vivo studies

INTRODUCTION

T-PLS (Twin-Pulse Life Support) is the first commercial pulsatile ECLS (Extra Corporeal Life Support) device (1). The dual sac structure of T-PLS can effectively reduce high membrane oxygenator inlet pressure and hemolysis. To verify both the use of T-PLS for ECLS and the advantages of T-PLS, we tested various models.

METHOD AND RESULTS

In the partial CPB (cardio pulmonary bypass) model (swine), T-PLS (N = 6), and Biopump (N = 2), a single pulsatile pump (N = 2), were compared. In the case of single pulsatile flow, during pump systole, pressure increased to 700 - 800 mmHg at the inlet port of the membrane oxygenator. fHb, a hemolysis measurement value, was about 80 mg/dL at 3 hours. On the contrary, because of T-PLS's dual sac system, the pressure of T-PLS had a maximum value of about 250 mmHg and fHb was similar to that of the commercial centrifugal pumps. In the total CPB model (bovine, N = 6), the heart was stopped via cardioplegia (Kcl). T-PLS flow was maintained at 3.0-4.5 L/min. T-PLS functioned like a natural heart, having a pulse pressure of 26-43 mmHg and a pulse rate of 40-60 bpm (beats per minute). In the emergency case model (canine, N = 6), T-PLS was started 10 minutes after cardiac arrest from electronic shock. In spite of cardiac arrest for a period of 40 minutes, the heart was recovered after defibrillation. In the ARDS (Acute Respiratory Distress Syndrome) model (canine, N = 6), minimal ventilator parameters were set: tidal volume 130 ml, respiration rate = bpm, FiO2 = 10%. Three hours after starting T-PLS, PO2 of the carotid artery blood (after 2 hours: 195 +/- 89.4; after 3 hours: 258 +/- 99.3 mmHg) was above half the value of the femoral artery but was within normal range.

CONCLUSION

It is suggested that a portable pulsatile ECLS like T-PLS may be used as a CPB device and as an alternative CPR (cardiopulmonary resuscitation) device in the case of cardiac arrest. Due to the pulsatile flow, oxygenated blood is delivered to the patient without overloading the ARDS patients heart.

Photocatalytic degradation of explosives contaminated water

This study was undertaken to examine the degradation of TNT, RDX and HMX in a circular photocatalytic reactor with TiO2 as a photocatalyst. We examined the impact of parameters such as the initial concentration, initial pH of solution on rates of photocatalized transformation, and the mineralization. The results showed that photocatalysis is an effective process for the degradation of TNT, RDX and HMX. They could be comoletely degraded in 150 min with 1.0 g/L TiO2 at pH 7. An increase in the photocatalytic degradation of HMX was noticed with decreasing initial HMX. The rates of RDX and HMX degradation were greater in neutral pH than in acidic and alkaline conditions. In case of TNT degradation, the rate of degradation was the fastest at pH 11. Approximately 82% TOC decrease in the TNT degradation was achieved after 150 min, whereas TOC decrease in RDX and HMX was 24% and 59%, respectively. Nitrate, nitrite, and ammonium ions were detected as the nitrogen byproducts from the photocatalysis, and more than 50% of the total nitrogen was recovered as nitrate ion in every explosives.

Novel fluorophores: efficient synthesis and photophysical study

[structure: see text] We have synthesized novel fluorophores by using Sonogashira reactions of 1,4-bis(dibromovinyl)benzene and 2,5-bis(dibromovinyl)thiophene with various aromatic bromides. The emission maxima of these fluorophores vary from the indigo blue to the reddish-orange region, depending on the structures of aromatic nuclei and peripheral moieties.

The effect of cilostazol on glucose tolerance and insulin resistance in a rat model of non-insulin dependent diabetes mellitus

BACKGROUND

It has been reported that many peripheral vasodilating drugs might improve insulin resistance. Cilostazol, a antithrombotic agent, increases peripheral blood flow in non-insulin dependent diabetic patients. The effect of cilostazol treatment on insulin resistance in streptozotocin (STZ)-induced non-insulin dependent diabetic Wistar rats was examined.

METHODS

About a half of two-day old neonate siblings were injected intraperitoneally with STZ and maintained for six months, at which time they were compared with age-matched control rats for intraperitoneal glucose tolerance test (IPGTT) and for glucose infusion rate (GINF) in a euglycemic hyperinsulinemic glucose-clamp study. After that, these studies were also performed after feeding rat chow containing cilostazol (100 mg/kg/day) to rats with STZ-induced non-insulin dependent diabetes mellitus for four-weeks and compared with those of age-matched control rats.

RESULTS

In the intraperitoneal glucose tolerance test studies, plasma glucose levels of STZ-induced non-insulin dependent diabetic rats were significantly higher and plasma insulin levels significantly lower than those of age-matched control rats in the age of six months. Glucose infusion rate was lower in STZ-induced non-insulin dependent diabetic rats than those of age-matched control rats. However, after a four-week cilostazol treatment, glucose infusion rate of STZ-induced non-insulin dependent diabetic rats was not significantly different from that of control rats.

CONCLUSION

These findings suggested that cilostazol may improve insulin resistance in STZ-induced non-insulin dependent diabetic rats.

Role of catalytic residues in enzymatic mechanisms of homologous ketosteroid isomerases

Ketosteroid isomerase (KSI) is one of the most proficient enzymes catalyzing an allylic isomerization reaction at a diffusion-controlled rate. In this study of KSI, we have detailed the structures of its active site, the role of various catalytic residues, and have explained the origin of the its fast reactivity by carrying out a detailed investigation of the enzymatic reaction mechanism. This investigation included the X-ray determination of 15 crystal structures of two homologous enzymes in free and complexed states (with inhibitors) and extensive ab initio calculations of the interactions between the active sites and the reaction intermediates. The catalytic residues, through short strong hydrogen bonds, play the role of charge buffer to stabilize the negative charge built up on the intermediates in the course of the reaction. The hydrogen bond distances in the intermediate analogues are found to be about 0.2 A shorter in the product analogues both experimentally and theoretically.

Simulation studies on bacteriorhodopsin bundle of transmembrane alpha segments

Bacteriorhodopsin (BR) is a membrane protein which pumps protons through the plasma membrane. Seven transmembrane BR helical segments are subjected to simulation studies in order to investigate the packing process of transmembrane helices. A Monte Carlo simulated annealing protocol is employed to optimize the helix bundle system. Helix packing is optimized according to a semi-empirical potential mainly composed of six components: a bilayer potential, a crossing angle potential, a helix dipole potential, a helix-helix distance potential, a helix orientation potential and a helix-helix distance restraint potential (a loop potential). Necessary parameters are derived from theoretical studies and statistical analysis of experimentally determined protein structures. The structures from the simulations are compared with the experimentally determined structures in terms of geometry. The structures generated show similar shapes to the experimentally suggested structure even without the helix-helix distance restraint potential. However, the relative locations of individual helices were reproduced only when the helix-helix distance restraint potential was used with restraint conditions. Our results suggest that transmembrane helix bundles resembling those observed experimentally may be generated by simulations using simple potentials.

Simulation studies on bacteriorhodopsin alpha-helices

Bacteriorhodopsin (BR) is a membrane protein which pumps protons through the plasma membrane. Transmembrane BR helical segments are subjected to simulation studies in order to investigate the effect of bilayer environment in various simulation conditions. A bilayer potential is introduced to the system to mimic the lipid membrane. The structures from the simulations are compared with the experimentally determined structures in terms of geometrical properties. Electrostatic contribution to the helix packing is also investigated. The simulation results show that the packing geometry of the transmembrane helices is highly affected by the bilayer potential. The results obtained from the simulations may be used for further simulation studies and analysis in investigating transmembrane helix packing.

Simulation of the packing of idealized transmembrane alpha-helix bundles

The aim of this study is to investigate if the packing motifs of native transmembrane helices can be produced by simulations with simple potentials and to develop a method for the rapid generation of initial candidate models for integral membrane proteins composed of bundles of transmembrane helices. Constituent residues are mapped along the helix axis in order to maintain the amino acid sequence-dependent properties of the helix. Helix packing is optimized according to a semi-empirical potential mainly composed of four components: a bilayer potential, a crossing angle potential, a helix dipole potential and a helix-helix distance potential. A Monte Carlo simulated annealing protocol is employed to optimize the helix bundle system. Necessary parameters are derived from theoretical studies and statistical analysis of experimentally determined protein structures. Preliminary testing of the method has been conducted with idealized seven Ala(20) helix bundles. The structures generated show a high degree of compactness. It was observed that both bacteriorhodopsin-like and delta-endotoxin-like structures are generated in seven-helix bundle simulations, within which the composition varies dependent upon the cooling rate. The simulation method has also been employed to explore the packing of N = 4 and N = 12 transmembrane helix bundles. The results suggest that seven and 12 transmembrane helix bundles resembling those observed experimentally (e.g., bacteriorhodopsin, rhodopsin and cytochrome c oxidase subunit I) may be generated by simulations using simple potentials.

The influenza A virus M2 channel: a molecular modeling and simulation study

The M2 protein of influenza virus forms ion channels activated by low pH which are proton permeable and play a key role in the life cycle of the virus. M2 is a 97-residue integral membrane protein containing a single transmembrane (TM) helix. M2 is present as disulfide-linked homotetramers. The TM domain of M2 has been modeled as a bundle of four parallel M2 helices. The helix bundle forms a left-handed supercoil surrounding a central pore. Residue H37 has been implicated in the mechanism of low-pH activation of the channel. Models generated with H37 in a fully deprotonated state exhibit a pore occluded by a ring of H37 side chains oriented toward the lumen of the pore. Models with H37 in a fully protonated state no longer exhibit such occlusion of the pore, as the H37 side chains adopt a more interfacial location. Extended molecular dynamics simulations with water molecules within and at the mouths of the pores support this distinction between the H37-deprotonated and H37-protonated models. These simulations suggest that only in the H37-protonated model is there a continuous column of water extending the entire length of the central pore. A mechanism for activation of M2 by low pH is presented in which the H37-deprotonated model corresponds to the "closed" form of the channel, while the H37-protonated model corresponds to the "open" form. A switch from the closed to the open form of the channel occurs if H37 is protonated midway through a simulation. The open channel is suggested to contain a wire of H-bonded water molecules which enables proton permeability.

Simulation studies of alamethicin-bilayer interactions

Alamethicin is an alpha-helical peptide that forms voltage-activated ion channels. Experimental data suggest that channel formation occurs via voltage-dependent insertion of alamethicin helices into lipid bilayers, followed by self-assembly of inserted helices to form a parallel helix bundle. Changes in the kink angle of the alamethicin helix about its central proline residue have also been suggested to play a role in channel gating. Alamethicin helices generated by simulated annealing and restrained molecular dynamics adopt a kink angle similar to that in the x-ray crystal structure, even if such simulations start with an idealized unkinked helix. This suggests that the kinked helix represents a stable conformation of the molecule. Molecular dynamics simulations in the presence of a simple bilayer model and a transbilayer voltage difference are used to explore possible mechanisms of helix insertion. The bilayer is represented by a hydrophobicity potential. An alamethicin helix inserts spontaneously in the absence of a transbilayer voltage. Application of a cis positive voltage decreases the time to insertion. The helix kink angle fluctuates during the simulations. Insertion of the helix is associated with a decrease in the mean kink angle, thus helping the alamethicin molecule to span the bilayer. The simulation results are discussed in terms of models of alamethicin channel gating.

Molecular dynamics simulations of isolated transmembrane helices of potassium channels

In the middle of the S6 helix in voltage-gated potassium channels there is a highly conserved Pro-Val-Pro motif, while the equivalent M2 helix of inward rectifier potassium channels contains a conserved glycine residue in a comparable position. The structural implications of these conserved motifs are of interest given the evidence that S6 and M2 are components of the lining of their respective pores. Multiple sequence alignment and TM helix prediction methods were used to define consensus regions for S6 and M2. Ensembles of 50 structures for each helix were generated by simulated annealing and restrained molecular dynamics. Time-dependent fluctuations of S6 and M2 were investigated by long time scale molecular dynamics simulations on representative members of each ensemble carried out in vacuo in the presence and absence of a hydrophobic potential that mimics a lipid bilayer. The results are discussed in terms of the structural basis of the kink in S6 and M2 and of a putative functional role for flexible helices as "molecular swivels."

Seven-helix bundles: molecular modeling via restrained molecular dynamics

Simulated annealing via restrained molecular dynamics (SA/MD) has been used to model compact bundles of seven approximately (anti)parallel alpha-helices. Seven such helix bundles occur, e.g., in bacteriorhodopsin, in rhodopsin, and in the channel-forming N-terminal domain of Bacillus thuringiensis delta-endotoxin. Two classes of model are considered: (a) those consisting of seven Ala20 peptide chains; and (b) those containing a single polypeptide chain, made up of seven Ala20 helices linked by GlyN interhelix loops (where N = 5 or 10). Three different starting C alpha templates for SA/MD are used, in which the seven helices are arranged (a) on a left-handed circular template, (b) on a bacteriorhodopsin-like template, or (c) on a zig-zag template. The ensembles of models generated by SA/MD are analyzed in terms of their geometry and energetics, and the most stable structures from each ensemble are examined in greater detail. Structures resembling bacteriorhodopsin and structures resembling delta-endotoxin are both represented among the most stable structures. delta-Endotoxin-like structures arise from both circular and bacteriorhodopsin-like C alpha templates. A third helix-packing mode occurs several times among the stable structures, regardless of the C alpha template and of the presence or absence of interhelix loops. It is characterized by a "4 + 1" core, in which four helices form a distorted left-handed supercoil around a central, buried helix. The remaining two helices pack onto the outside of the core. This packing mode is comparable with that proposed for rhodopsin on the basis of two-dimensional electron crystallographic and sequence analysis studies.

Cascade control of Escherichia coli glutamine synthetase. Purification and properties of PII protein and nucleotide sequence of its structural gene

A procedure was developed to purify large quantities of PII protein from an Escherichia coli strain which contains a multicopy plasmid harboring the structural gene of PII (the glnB gene). Ultraviolet spectra of uridylylated and unuridylylated PII were obtained using the purified PII and empirical formulas to calculate the concentration of protein and the average number of uridylylated subunits per molecule were derived. A continuous fluorometric assay for the measurement of uridylylated PII (PIID) and adenylyltransferase (ATase) was also established. Rate measurements at various concentrations of PIID and at a fixed concentration of ATase showed that a tetrameric PIID molecule interacts with only one ATase molecule at a time. The complete nucleotide sequence of the glnB gene was determined and parts of the deduced amino acid sequence were confirmed by the results of amino acid sequence analysis of peptides. The PII subunit consists of 103 amino acids (Mr = 11,580). Two tyrosines reside at positions 46 and 51, where Tyr51 is the site of uridylylation. Nucleotide sequence analysis of the upstream region showed no obvious sites for the binding of RNA polymerase, indicating that the glnB gene is a part of an as yet unidentified operon.