CHARMM: the biomolecular simulation program

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

Presentation and management of perineal endometriosis

OBJECTIVE

To analyze the clinical presentation of perineal endometriosis and evaluate its treatment.

METHODS

Clinical data were analyzed from the records of 36 patients with perineal endometriosis who were operated on between 1983 and 2007 at Peking Union Medical College Hospital, and followed up for 0.5 to 14 years.

RESULTS

The incidence of perineal endometriosis was 0.31% among the women with endometriosis treated surgically at the hospital. The latent period was between 4 months and 13 years. All patients had cyclical and painful lesions. Of the 36 patients, 5 (13.9%) also suffered from pelvic endometriosis. All patients without anal sphincter involvement were cured after complete surgical excision. In 7 patients who had anal sphincter involvement, disease recurred because of incomplete excision.

CONCLUSION

Perineal endometriosis can be diagnosed on the basis of clinical features and surgical excision is the treatment of choice. The recurrence rate of perineal endometriosis is related to sphincter involvement making preoperative evaluation of anal sphincter important.

The role of macrophages in optic nerve regeneration

Following injury to the nervous system, the activation of macrophages, microglia, and T-cells profoundly affects the ability of neurons to survive and to regenerate damaged axons. The primary visual pathway provides a well-defined model system for investigating the interactions between the immune system and the nervous system after neural injury. Following damage to the optic nerve in mice and rats, retinal ganglion cells, the projection neurons of the eye, normally fail to regenerate their axons and soon begin to die. Induction of an inflammatory response in the vitreous strongly enhances the survival of retinal ganglion cells and enables these cells to regenerate lengthy axons beyond the injury site. T cells modulate this response, whereas microglia are thought to contribute to the loss of retinal ganglion cells in this model and in certain ocular diseases. This review discusses the complex and sometimes paradoxical actions of blood-borne macrophages, resident microglia, and T-cells in determining the outcome of injury in the primary visual pathway.

The Effects of Open Lung Ventilation on Respiratory Mechanics and Haemodynamics in Atelectatic Infants after Cardiopulmonary Bypass

Acute lung injury (ALI) frequently occurs in infants after cardiopulmonary bypass (CPB) surgery and it sometimes develops into acute respiratory distress syndrome in critically ill infants, which can be life threatening. This study investigated the effects of open lung ventilation on the haemodynamics and respiratory mechanics of 64 infants (34 males; 30 females) with a mean ± SD age of 8.3 ± 0.3 months who developed ALI following CPB surgery. Open lung ventilation significantly improved the respiratory mechanics and oxygenation parameters of the infants, including the partial pressure of oxygen in arterial blood (PaO2), the ratio of PaO2/FiO2 (fraction of inspired oxygen), peak inspiratory pressure, static compliance and airway resistance. It is concluded that open lung ventilation can greatly improve oxygenation and respiratory mechanics in infants with ALI following CPB surgery.

Differentiation block of oligodendroglial progenitor cells as a cause for remyelination failure in chronic multiple sclerosis

Impaired function/differentiation of progenitor cells might provide an explanation for the limited remyelination observed in the majority of chronic multiple sclerosis lesions. Here, we establish that in the normal adult human CNS, the transcription factors Nkx2.2 and Olig2 are strongly expressed in progenitor cells while mature oligodendrocytes are characterized by low levels of Olig2 or Nkx2.2. In vitro studies confirmed the expression of Olig2 in oligodendroglial progenitor cells and mature oligodendrocytes while astrocytes, microglial cells and neurons were negative for Olig2. In early multiple sclerosis lesions, we found Olig2-positive progenitor cells throughout all lesion stages and in periplaque white matter (PPWM). The number of progenitors in PPWM was significantly increased compared with the white matter from controls. In chronic multiple sclerosis lesions progenitor cells were still present, however, in significantly lower numbers than in early multiple sclerosis lesions. A subpopulation of progenitor cells in early multiple sclerosis lesions and PPWM but not in control cases co-expressed NogoA, a marker of mature oligodendrocytes. The co-expression of these two markers suggested that these cells were maturing oligodendrocytes recently recruited from the progenitor pool. In contrast, in chronic multiple sclerosis lesions maturing progenitors were only rarely present. In summary, we provide evidence that a differentiation block of oligodendroglial progenitors is a major determinant of remyelination failure in chronic multiple sclerosis lesions.

Possible role of hydrogen sulfide on the preservation of donor rat hearts

OBJECTIVE

The aim of this study was to observe the preservative effect of hydrogen sulfide (H2S) on donor rat hearts.

MATERIALS AND METHODS

The hearts of 24 Sprague-Dawley rats were perfused on a Langendorff perfusion column for 30 minutes. We calculated and recorded the left ventricular-developed pressure (LVDP), and positive and negative derivatives of left ventricular systolic pressure (LVSP; +dP/dt and -dP/dt). Hearts were then arrested and stored for 6 hours at 4 degrees C: group 1, Krebs-Henseleit (KH) solution; group 2, KH solution with 1 micromol/L NaHS; group 3, KH solution with 1 micromol/L NaHS and 10 micromol/L glibenclamide; group 4, St. Thomas II solution. Hearts were transferred back to the Langendorff column. After stabilizing for 30 minutes, LV performance was assessed as before. The donor hearts were kept for pathological study including myocardial water ratio, ATP content, and myocyte apoptosis index.

RESULTS

The recovery rates of +dp/dtmax, -dp/dtmax, and LVDP of groups 2 and 4 were much better than those of groups 1 and 3. The hearts contracted immediately after reperfusion in group 4. Ventricular fibrillation was seen before contraction in the other 3 groups, with the longest duration in group. No significant difference in myocardial water ratio was found. The ATP content was the highest in group 2. Apoptosis was observed in the 4 groups with the lowest apoptosis index in group 2.

CONCLUSIONS

H2S has a protective effect on rat donor hearts at the concentration of 1 micromol/L. The protective effect is better than that of St. Thomas II solution. The protective effect of H2S can be blocked by glibenclamide.

Differential roles of phosphatidylinositol 3-kinase/akt pathway in retinal ganglion cell survival in rats with or without acute ocular hypertension

Intraocular pressure (IOP) elevation has often been used as an experimental model to study mechanisms underlying retinal ganglion cell (RGC) death associated with ocular ischemic injury and glaucoma. The aim of the present study, using both in vitro and in vivo approaches, was to investigate the role of phosphatidylinositol 3-kinase (PI3K)/akt pathway in RGC viability in normal rats and rats following transient IOP elevation. For in vivo studies, pathway inhibitors were administered intravitreally on days 3, 9, and 15 post-2-h IOP elevation at 110 mm Hg. Toward the end of the 3-week examination period, the fluorescent dye Fluorogold was used to retrogradely label surviving RGCs. In order to examine the role of macrophages that were recruited into the eye following the pathway inhibition, clodronate liposomes were used to deplete phagocytic cells in the eye. PI3K/akt pathway activity and location in the retina were examined using Western blot and immunohistochemistry, respectively. Here we showed that PI3K/akt inhibitors 2-(4-morpholinyl)-8-phenyl-1(4H)-benzopyran-4-one hydrochloride (LY294002) and KY12420 at low concentrations (2 microM or 20 microM) did not influence RGC survival but caused RGC loss at high concentration (200 muM) in retinal explants derived from intact rats. In contrast, both LY294002 and KY12420 at 20 microM led to RGC loss in retinal explants derived from IOP-elevated eyes. A detrimental action of phagocytic cells on RGC survival was also seen in these retinas. In vivo results confirmed the detrimental actions of PI3K/akt inhibition and macrophages on RGC survival in IOP-elevated, but not intact eyes even with high concentration of LY294002. Low level of PI3K/akt activity was detected in the ganglion cell layer (GCL) in intact retina. Acute IOP elevation activated PI3K/akt pathway in the inner nuclear layer and GCL including RGCs. This study thus demonstrates that PI3K/akt pathway mediates RGC survival after IOP elevation but not under normal condition.

Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network

Mutations or overexpression of signalling genes can result in cancer development and metastasis. In this study, we manually assembled a human cellular signalling network and developed a robust bioinformatics strategy for extracting cancer-associated single nucleotide polymorphisms (SNPs) using expressed sequence tags (ESTs). We then investigated the relationships of cancer-associated genes [cancer-associated SNP genes, known as cancer genes (CG) and cell mobility genes (CMGs)] in a signalling network context. Through a graph-theory-based analysis, we found that CGs are significantly enriched in network hub proteins and cancer-associated genes are significantly enriched or depleted in some particular network motif types. Furthermore, we identified a substantial number of hotspots, the three- and four-node network motifs in which all nodes are either CGs or CMGs. More importantly, we uncovered that CGs are enriched in the convergent target nodes of most network motifs, although CMGs are enriched in the source nodes of most motifs. These results have implications for the foundations of the regulatory mechanisms of cancer development and metastasis.

A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method

The performance of different link atom based frontier treatments in QM/MM simulations was evaluated critically with SCC-DFTB as the QM method. In addition to the analysis of gas-phase molecules as in previous studies, an important element of the present work is that chemical reactions in realistic enzyme systems were also examined. The schemes tested include all options available in the program CHARMM for SCC-DFTB/MM simulation, which treat electrostatic interactions due to the MM atoms close to the QM/MM boundary in different ways. In addition, a new approach, the divided frontier charge (DIV), has been implemented in which the partial charge associated with the frontier MM atom ("link host") is evenly distributed to the other MM atoms in the same group. The performance of these schemes was evaluated based on properties including proton affinities, deprotonation energies, dipole moments, and energetics of proton transfer reactions. Similar to previous work, it was found that calculated proton affinities and deprotonation energies of alcohols, carbonic acids, amino acids, and model DNA bases are very sensitive to the link atom scheme; the commonly used single link atom approach often gives error on the order of 15 to 20 kcal/mol. Other schemes give better and, on average, mutually comparable results. For proton transfer reactions, encouragingly, both activation barriers and reaction energies are fairly insensitive (within a typical range of 2-4 kcal/mol) to the link atom scheme due to error cancellation, and this was observed for both gas-phase and enzyme systems. Therefore, the effect of using different link atom schemes in QM/MM simulations is rather small for chemical reactions that conserve the total charge. Although the current study used an approximate DFT method as the QM level, the observed trends are expected to be applicable to QM/MM methods with use of other QM approaches. This observation does not mean to encourage QM/MM simulations without careful benchmark in the study of specific systems, rather it emphasizes that other technical details, such as the treatment of long-range electrostatics, tend to play a more important role and need to be handled carefully.

Strain-specific differences in the effects of cyclosporin A and FK506 on the survival and regeneration of axotomized retinal ganglion cells in adult rats

The immune response can influence neuronal viability and plasticity after injury, effects differing in strains of rats with different susceptibility to autoimmune disease. We assessed the effects of i.p. injections of cyclosporin A (CsA) or FK506 on adult retinal ganglion cell (RGC) survival and axonal regeneration into peripheral nerve (PN) autografted onto the cut optic nerve of rats resistant (Fischer F344) or vulnerable (Lewis) to autoimmune disease. Circulating and tissue CsA and FK506 levels were similar in both strains. Three weeks after autologous PN transplantation the number of viable beta-III tubulin-positive RGCs was significantly greater in CsA- and FK506-treated F344 rats compared with saline-injected controls. RGC survival in Lewis rats was not significantly altered. In F344 rats, retrograde labeling of RGCs revealed that CsA or FK506 treatment significantly increased the number of RGCs that regenerated an axon into a PN autograft; however these agents had no beneficial effect on axonal regeneration in Lewis rats. PN grafts in F344 rats also contained comparatively more pan-neurofilament immunoreactive axons. In both strains, 3 weeks after transplantation CsA or FK506 treatment resulted in increased retinal macrophage numbers, but only in F344 rats was this increase significant. At this time-point PN grafts in both strains contained many macrophages and some T cells. T cell numbers in Lewis rats were significantly greater than in F344 animals. The increased RGC axonal regeneration seen in CsA- or FK506-treated F344 but not Lewis rats shows that modulation of immune responses after neurotrauma has complex and not always predictable outcomes.

Administration of donor-derived mesenchymal stem cells can prolong the survival of rat cardiac allograft

BACKGROUND

Mesenchymal stem cells (MSCs) are multipotent adult elements that have recently been shown to have profound immunomodulatory effects both in vitro and in vivo. Herein we have examined the impact of intravenous infusion of donor MSCs on the survival of transplanted hearts in a rat allograft model.

METHODS

Recipient Fisher344 rats were transplanted with hearts from inbred Wistar rats. Wistar rat MSCs were infused via the tail vein at designated intervals. In vitro mixed lymphocyte reaction (MLR) and cell-mediated lympholysis (CML) assays were performed to assess whether MSCs downregulated T-cell responses in vivo. Real-time polymerase chain reaction (PCR) was used to analyze the Th1/Th2 balance in MSC-treated and control groups.

RESULTS

The MSCs cultured in vitro exhibited multipotential for differentiation. Survival of the allografts was markedly prolonged by administration of MSCs compared with the controls, namely mean survivals of 12.4 vs 6.4 days, respectively. Real-time PCR showed a shift in the Th1/Th2 balance toward Th2. By MLR and CML assays, untreated control rats showed greater alloreactivity than did MSC-treated rats.

CONCLUSION

Our results indicated that MSCs suppressed allogeneic T-cell responses both in vitro and in vivo. Intravenous administration of MSCs prolonged the survival of transplanted hearts, possibly by induction of allograft tolerance through changing the Th1/Th2 balance.

Dynamics of X+CH4 (X=H,O,Cl) reactions: How reliable is transition state theory for fine-tuning potential energy surfaces?

Trajectory calculations run on global potential energy surfaces have shown that the topology of the entrance channel has strong implications on the dynamics of the title reactions. This may explain why huge differences are observed between the rate constants calculated from global dynamical methods and those obtained from local methods that employ the same potential energy surfaces but ignore such topological details. Local dynamics approaches such as transition state-based theories should then be used with caution for fine-tuning potential energy surfaces, especially for fast reactions with polyatomic species since the key statistical assumptions of the theory may not be valid for all degrees of freedom.

AAV-mediated expression of CNTF promotes long-term survival and regeneration of adult rat retinal ganglion cells

We compared the effects of intravitreal injection of bi-cistronic adeno-associated viral (AAV-2) vectors encoding enhanced green fluorescent protein (GFP) and either ciliary neurotrophic factor (CNTF), brain-derived neurotrophic factor (BDNF) or growth-associated protein-43 (GAP43) on adult retinal ganglion cell (RGC) survival and regeneration following (i) optic nerve (ON) crush or (ii) after ON cut and attachment of a peripheral nerve (PN). At 7 weeks after ON crush, quantification of betaIII-tubulin immunostaining revealed that, compared to AAV-GFP controls, RGC survival was not enhanced by AAV-GAP43-GFP but was increased in AAV-CNTF-GFP (mean RGCs/retina: 17 450+/-358 s.e.m.) and AAV-BDNF-GFP injected eyes (10 200+/-4064 RGCs/retina). Consistent with increased RGC viability in AAV-CNTF-GFP and AAV-BDNF-GFP injected eyes, these animals possessed many betaIII-tubulin- and GFP-positive fibres proximal to the ON crush. However, only in the AAV-CNTF-GFP group were regenerating RGC axons seen in distal ON (1135+/-367 axons/nerve, 0.5 mm post-crush), some reaching the optic chiasm. RGCs were immunoreactive for CNTF and quantitative RT-PCR revealed a substantial increase in CNTF mRNA expression in retinas transduced with AAV-CNTF-GFP. The combination of AAV-CNTF-GFP transduction of RGCs with autologous PN-ON transplantation resulted in even greater RGC survival and regeneration. At 7 weeks after PN transplantation there were 27 954 (+/-2833) surviving RGCs/retina, about 25% of the adult RGC population. Of these, 13 352 (+/-1868) RGCs/retina were retrogradely labelled after fluorogold injections into PN grafts. In summary, AAV-mediated expression of CNTF promotes long-term survival and regeneration of injured adult RGCs, effects that are substantially enhanced by combining gene and cell-based therapies/interventions.

Application of I125 Brachytherapy Combined Artificial Joint Prosthesis in Malignant Osteo- and Soft-Tissue Sarcoma

OBJECTIVES

The aim of this study was to evaluate the brachytherapy effectiveness of I(125) seeds combined with artificial prosthesis in malignant sarcoma therapy.

METHODS

The combination of I(125) seeds and artificial prosthesis was implanted to replace tumor section for three clinical cases-2 malignant osteosarcoma patients and 1 malignant soft-tissue tumor patient- through the direct operation.

RESULTS

Approximately 14-18 months after the operation, the results of our post-operational investigation showed that the tumor tissues of 3 patients had been completely removed. The limb functions recovered well. The brachytherapy of the combination of I(125) seeds and artificial prosthesis in malignant tumor improved the curative effect. No tumor existed, and no infection occurred.

CONCLUSIONS

It was demonstrated that this method was safe and easy. No side-effect was observed after the implantation of I(125) seeds. The brachytherapy was proven to be a potential method for patients who were at high risk to recrudesce the malignant osteosarcoma of tumors after the tumor excision.

SEA0400, a novel Na+/Ca2+ exchanger inhibitor, reduces calcium overload induced by ischemia and reperfusion in mouse ventricular myocytes

Given the potential clinical benefit of inhibiting Na+/Ca2+ exchanger (NCX) activity during myocardial ischemia reperfusion (I/R), pharmacological approaches have been pursued to both inhibit and clarify the importance of this exchanger. SEA0400 was reported to have a potent NCX selectivity. Thus, we examined the effect of SEA0400 on NCX currents and I/R induced intracellular Ca2+ overload in mouse ventricular myocytes using patch clamp techniques and fluorescence measurements. Ischemia significantly inhibited inward and outward NCX current (from -0.04+/-0.01 nA to 0 nA at -100 mV; from 0.23+/-0.08 nA to 0.11+/-0.03 nA at +50 mV, n=7), Subsequent reperfusion not only restored the current rapidly but enhanced the current amplitude obviously, especially the outward currents (from 0.23+/-0.08 nA to 0.49+/-0.12 nA at +50 mV, n=7). [Ca2+]i, expressed as the ratio of Fura-2 fluorescence intensity, increased to 138+/-7% (P<0.01) during ischemia and to 210+/-11% (P<0.01) after reperfusion. The change of NCX current and the increase of [Ca2+]i during I/R can be blocked by SEA0400 in a dose-dependent manner with an EC50 value of 31 nM and 28 nM for the inward and outward NCX current, respectively. The results suggested that SEA0400 is a potent NCX inhibitor, which can protect mouse cardiac myocytes from Ca2+ overload during I/R injuries.

Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps

Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of quantum mechanics-molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.

cAMP regulates axon outgrowth and guidance during optic nerve regeneration in goldfish

Increased cAMP improves neuronal survival and axon regeneration in mammals. Here, we assess cAMP levels and identify activated pathways in a spontaneously regenerating central nervous system. Following optic nerve crush in goldfish, almost all retinal ganglion cells (RGC) survive and regenerate retinotectal topography. Goldfish received injections of a cAMP analogue (CPT-cAMP), a protein kinase A (PKA) inhibitor (KT5720), both compounds combined, or PBS (control). RGC survival in experimental groups was unaffected at any stage. The rate of axon regeneration was accelerated by the activator and decelerated both by the inhibitor and by combined injections, suggesting a PKA-dependent pathway. In addition, errors in regenerate retinotectal topography were observed when agents were applied in vivo and RGC response to the guidance cue ephrin-A5 in vitro was altered by the inhibitor. Our results highlight that therapeutic manipulation of cAMP levels to enhance axonal regeneration in mammals must ensure that topography, and consequently function, is not disrupted.

Retinal ganglion cell neurotrophin receptor levels and trophic requirements following target ablation in the neonatal rat

Superior colliculus (SC) ablation in neonatal rats results in a rapid increase in retinal ganglion cell (RGC) death. This injury-induced death is reduced by exogenous brain-derived neurotrophic factor or neurotrophin-4/5 (NT-4/5), but the protective effect of these molecules is transient, delaying but not preventing neuronal loss. We sought to discover why neurotrophins only temporarily reduce RGC death after target ablation, focusing on changes in neurotrophin receptor expression and possible changes in growth factor dependency. In unlesioned rats, receptor tyrosine kinase B (trkB) immunohistochemistry revealed no change in the number of trkB positive cells in the RGC layer 24 h after intraocular NT-4/5 injection. However, after SC lesions there were significantly less immunoreactive cells and, surprisingly, even fewer immunoreactive cells in NT-4/5 injected eyes. Semi-quantitative confocal analysis of immunofluorescence intensity revealed an increase in trkB staining in the RGC layer in unlesioned rats 24 h after NT-4/5 injection, whereas in SC-lesioned animals exposed to NT-4/5 there was a significant decrease in staining. To determine whether injured neonatal RGCs can switch their trophic requirements, different doses of ciliary neurotrophic factor were given intraocularly, either alone or combined with NT-4/5. We also tested an SC-derived chondroitin sulfate proteoglycan that has been reported to promote neonatal RGC survival. None of these interventions reduced lesion-induced RGC death 24 or 36 h after SC ablation. In summary, we show that developing RGCs do not shift their trophic dependence to other survival factors following injury; rather, the application of neurotrophins causes a down-regulation of the cognate trkB receptor, presumably altering the long-term responsiveness of neonatal RGCs to exogenous neurotrophins. These data highlight the difficulty in promoting long-term neuronal survival when using one-off administration of recombinant growth factors.

Uterine adenomyoma with lymphoid infiltration simulating lymphoma

BACKGROUND

Uterine leiomyoma with lymphoid infiltration is a rare disease that simulates malignant lymphoma with only nine cases reported to date. We describe the first case of uterine adenomyoma with lymphoid infiltration simulating lymphoma.

CASE

The specimen resected from a 30-year-old Chinese woman was a well-defined firm nodule measuring 5 x 5.5 x 5.5 cm. The cut surface was similar to that of adenomyoma, which contained dark brown spots and a cyst. Microscopically, the tumor comprised smooth muscle cells intermixed with many lymphocytes. Many lymphoid follicles were present, just locating beside one side of thin-walled blood vessels and protruding into the vessels. Endometrial-type glands and stroma were visible in the tumor.

CONCLUSION

We describe the first case of uterine adenomyoma with lymphoid infiltration simulating lymphoma.