Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses.

The revolution in cryo-electron microscopy has resulted in unprecedented power to resolve large macromolecular complexes including viruses. Many methods exist to explain density corresponding to proteins and thus entire protein capsids have been solved at the all-atom level. However methods for nucleic acids lag behind, and no all-atom viral double-stranded DNA genomes have been published at all. We here present a method which exploits the spiral winding patterns of DNA in icosahedral capsids. The method quickly generates shells of DNA wound in user-specified, idealized spherical or cylindrical spirals. For transition regions, the method allows guided semiflexible fitting. For the kuravirus SU10, our method explains most of the density in a semiautomated fashion. The results suggest rules for DNA turns in the end caps under which two discrete parameters determine the capsid inner diameter. We suggest that other kuraviruses viruses may follow the same winding scheme, producing a discrete rather than continuous spectrum of capsid inner diameters. Our software may be used to explain the published density maps of other double-stranded DNA viruses and uncover their genome packaging principles.

Amino acid substitutions in human growth hormone affect secondary structure and receptor binding.

The interaction between human Growth Hormone (hGH) and hGH Receptor (hGHR) has basic relevance to cancer and growth disorders, and hGH is the scaffold for Pegvisomant, an anti-acromegaly therapeutic. For the latter reason, hGH has been extensively engineered by early workers to improve binding and other properties. We are particularly interested in E174 which belongs to the hGH zinc-binding triad; the substitution E174A is known to significantly increase binding, but to now no explanation has been offered. We generated this and several computationally-selected single-residue substitutions at the hGHR-binding site of hGH. We find that, while many successfully slow down dissociation of the hGH-hGHR complex once bound, they also slow down the association of hGH to hGHR. The E174A substitution induces a change in the Circular Dichroism spectrum that suggests the appearance of coiled-coiling. Here we show that E174A increases affinity of hGH against hGHR because the off-rate is slowed down more than the on-rate. For E174Y (and certain mutations at other sites) the slowdown in on-rate was greater than that of the off-rate, leading to decreased affinity. The results point to a link between structure, zinc binding, and hGHR-binding affinity in hGH.

A new diterpene and bioactivities of labdanes isolated from Buddleja marrubiifolia.

The new labdane [(3R*,4aR*,7S*,10aS*,10bR*)-3-ethenyl-3,4a,7,10a-tetramethyl-dodecahydro-1H-naphtho-[2,1-b]-pyran-7-yl]-methylbenzoate together with other 7 labdanes were isolated from the aerial parts of Buddleja marrubiifolia. Compound structures were elucidated by spectroscopic methods. Some compounds showed moderate to weak antimicrobial activity towards a panel of bacterial and fungal pathogens. In addition, trans-biformene (2) and ribenol acetate (8) showed to be highly cytotoxic with LC50 < 1 µg/mL, the other compounds showed moderate cytotoxic effect with a LC50 range of 6.008-15.26 µg/mL. For all isolated compounds, no inflammatory response was observed.

Mining the Protein Data Bank to improve prediction of changes in protein-protein binding.

Predicting the effect of mutations on protein-protein interactions is important for relating structure to function, as well as for in silico affinity maturation. The effect of mutations on protein-protein binding energy (ΔΔG) can be predicted by a variety of atomic simulation methods involving full or limited flexibility, and explicit or implicit solvent. Methods which consider only limited flexibility are naturally more economical, and many of them are quite accurate, however results are dependent on the atomic coordinate set used. In this work we perform a sequence and structure based search of the Protein Data Bank to find additional coordinate sets and repeat the calculation on each. The method increases precision and Positive Predictive Value, and decreases Root Mean Square Error, compared to using single structures. Given the ongoing growth of near-redundant structures in the Protein Data Bank, our method will only increase in applicability and accuracy.

Molecular Dynamics Simulations Suggest a Non-Doublet Decoding Model of -1 Frameshifting by tRNASer3.

In-frame decoding in the ribosome occurs through canonical or wobble Watson-Crick pairing of three mRNA codon bases (a triplet) with a triplet of anticodon bases in tRNA. Departures from the triplet-triplet interaction can result in frameshifting, meaning downstream mRNA codons are then read in a different register. There are many mechanisms to induce frameshifting, and most are insufficiently understood. One previously proposed mechanism is doublet decoding, in which only codon bases 1 and 2 are read by anticodon bases 34 and 35, which would lead to -1 frameshifting. In E. coli, tRNASer3GCU can induce -1 frameshifting at alanine (GCA) codons. The logic of the doublet decoding model is that the Ala codon's GC could pair with the tRNASer3's GC, leaving the third anticodon residue U36 making no interactions with mRNA. Under that model, a U36C mutation would still induce -1 frameshifting, but experiments refute this. We perform all-atom simulations of wild-type tRNASer3, as well as a U36C mutant. Our simulations revealed a hydrogen bond between U36 of the anticodon and G1 of the codon. The U36C mutant cannot make this interaction, as it lacks the hydrogen-bond-donating H3. The simulation thus suggests a novel, non-doublet decoding mechanism for -1 frameshifting by tRNASer3 at Ala codons.

Hydrogel-embedded gold nanorods activated by plasmonic photothermy with potent antimicrobial activity.

Plasmonic photothermal therapy (PPTT) has been used as an alternative to chemotherapy for the elimination of resistant microorganisms; however, its in situ evaluation has not been well studied. In the present study, we assessed the antimicrobial activity of a chitosan-based hydrogel embedded with gold nanorods (Ch/AuNRs) using a low power infrared diode laser. The antibacterial activity was measured in both Gram-positive and -negative strains, including clinical isolates of multidrug-resistant pathogens. The cytotoxic effect, cellular proliferation, and the expression of the pro-inflammatory (IL-6 and TNF-α) and anti-inflammatory (IL-10) cytokines were quantified in a murine model of macrophages. Results showed a potent antimicrobial activity of the Ch/AuNRs with MICs ≤4 µg/mL, very low cytotoxicity with cell viability above 80%, and the macrophage proliferation was not affected for a period of 48 h. These results suggest that our Ch/AuNR-embedded hydrogel could be an option to locally control chronic nosocomial infections using PPTT.

Treatment of hepatocarcinoma with celecoxib and pentoxifylline: a case report / Manejo del hepatocarcinoma con celecoxib y pentoxifilina: reporte de un caso

Background: Hepatocellular carcinoma (HCC) is the sixth most frequent tumor worldwide and it is responsible for approximately 750 000 deaths each year. It is the third leading cause of cancer death in Mexico. Despite the existing therapeutic regimens, HCC has a poor prognosis with a life expectancy of approximately one month in advanced cases. The use of celecoxib and pentoxifylline has recently been reported in tumor patients with promising results due to its anti-inflammatory, antiangiogenic, antifibrotic and proapoptotic effects. Nonetheless, the combination of both drugs for the treatment of HCC has never been employed. Clinical case: 58-year-old male patient, who arrived to the examination room for presenting nausea, jaundice, asthenia, adynamia and encephalopathy grade I-II. The patient had a history of alcoholism for 47 years and diagnosis of cirrhosis in Child C stage. An image with focal lesion in the right lobe of 8 x 8 cm, which was highly vascularized, suggested HCC by means of imaging studies (ultrasound, computed axial tomography [CAT] and magnetic resonance imaging). Management began in January, 2015, and continues until today with 400 mg of pentoxifylline every 12 hours, 200 mg of celecoxib every 12 hours and vitamin supplements. Conclusion: After one month, patient showed a surprising response, reduction in tumor size almost in its entirety, improvement of clinical condition, and turned into Child A stage. Eight months after treatment it was observed by CAT that the tumor had practically disappeared. Patient has survived for more than two years. These results are encouraging; however, it is necessary to conduct multicenter studies that prove the efficacy of the treatment.

Introducción: El hepatocarcinoma (HPC) es el sexto tumor más frecuente a nivel mundial y provoca aproximadamente 750 000 muertes al año. Representa la tercera causa de muerte por cáncer en México. A pesar de los esquemas terapéuticos existentes, el pronóstico en el HPC es malo, con un promedio aproximado de vida de un mes en casos avanzados. Recientemente se ha reportado el uso de celecoxib y pentoxifilina en pacientes tumorales con resultados prometedores debido a sus efectos antiinflamatorios, antiangiogénicos, antifibróticos y proapoptóticos. Sin embargo, nunca han sido usados en combinación para el tratamiento de HPC. Caso clínico: Paciente masculino de 58 años que acudió a consulta por presentar náuseas, ictericia, astenia, adinamia y encefalopatía grado I-II; tenía antecedente de alcoholismo durante 47 años y diagnóstico de cirrosis en estadio Child C. Mediante ultrasonido, tomografía axial computarizada (TAC) y resonancia magnética se evidenció una imagen con lesión focal en lóbulo derecho de 8 x 8 cm, altamente vascularizada, sugestiva de HPC. Se inició manejo en enero de 2015 y el paciente continúa hasta la fecha con pentoxifilina (400 mg/12 h), celecoxib (200 mg/12 h) y suplementos vitamínicos. Conclusión: Después de un mes el paciente mostró una respuesta sorprendente, reducción del tamaño de la lesión casi en su totalidad, mejoría del estadio clínico y cambió a un estadio Child A. Ocho meses después de implementar el tratamiento se observó por medio de TAC que el tumor casi había desaparecido. El paciente ha sobrevivido por más de dos años. Los resultados son alentadores; sin embargo, es necesario realizar estudios multicéntricos que demuestren su real eficacia.

Insights from engineering the Affibody-Fc interaction with a computational-experimental method.

The interaction between the Staphylococcal Protein A (SpA) domain B (the basis of the Affibody) molecule and the Fc of IgG is key to the use of Affibodies in affinity chromatography and in potential therapies against certain inflammatory diseases. Despite its importance and four-decade history, to our knowledge this interaction has never been affinity matured. We elucidate reasons why single-substitutions in the SpA which improve affinity to Fc may be very rare, and also discover substitutions which potentially serve several engineering purposes. We used a variation of FoldX to predict changes in protein-protein-binding affinity, and produce a list of 41 single-amino acid substitutions on the SpA molecule, of which four are near wild type (wt) and five are at most a factor of four from wt affinity. The nine substitutions include one which removes lysine, and several others which change charge. Subtle modulations in affinity may be useful for modifying column elution conditions. The method is applicable to other protein-protein systems, providing molecular insights with lower workload than existing experimental techniques.

Hospital-Level Variation in Practice Patterns and Patient Outcomes for Pediatric Patients Hospitalized With Functional Constipation.

BACKGROUND AND OBJECTIVE: Constipation is a common pediatric condition with a prevalence of 3% to 5% in children aged 4 to 17 years. Currently, there are no evidence-based guidelines for the management of pediatric patients hospitalized with constipation. The primary objective was to evaluate practice patterns and patient outcomes for the hospital management of functional constipation in US children's hospitals. METHODS: We conducted a multicenter, retrospective cohort study of children aged 0 to 18 years hospitalized for functional constipation from 2012 to 2014 by using the Pediatric Health Information System. Patients were included by using constipation and other related diagnoses as classified by International Classification of Diseases, Ninth Revision. Patients with complex chronic conditions were excluded. Outcome measures included percentage of hospitalizations due to functional constipation, therapies used, length of stay, and 90-day readmission rates. Statistical analysis included means with 95% confidence intervals for individual hospital outcomes. RESULTS: A total of 14 243 hospitalizations were included, representing 12 804 unique patients. The overall percentage of hospitalizations due to functional constipation was 0.65% (range: 0.19%-1.41%, P < .0001). The percentage of patients receiving the following treatment during their hospitalization included: electrolyte laxatives: 40% to 96%; sodium phosphate enema: 0% to 64%; mineral oil enema: 0% to 61%; glycerin suppository: 0% to 37%; bisacodyl 0% to 47%; senna: 0% to 23%; and docusate 0% to 11%. Mean length of stay was 1.97 days (range: 1.31-2.73 days, P < .0001). Mean 90-day readmission rate was 3.78% (range: 0.95%-7.53%, P < .0001). CONCLUSIONS: There is significant variation in practice patterns and clinical outcomes for pediatric patients hospitalized with functional constipation across US children's hospitals. Collaborative initiatives to adopt evidence-based best practices guidelines could help standardize the hospital management of pediatric functional constipation.

Modeling and fitting protein-protein complexes to predict change of binding energy.

It is possible to accurately and economically predict change in protein-protein interaction energy upon mutation (ΔΔG), when a high-resolution structure of the complex is available. This is of growing usefulness for design of high-affinity or otherwise modified binding proteins for therapeutic, diagnostic, industrial, and basic science applications. Recently the field has begun to pursue ΔΔG prediction for homology modeled complexes, but so far this has worked mostly for cases of high sequence identity. If the interacting proteins have been crystallized in free (uncomplexed) form, in a majority of cases it is possible to find a structurally similar complex which can be used as the basis for template-based modeling. We describe how to use MMB to create such models, and then use them to predict ΔΔG, using a dataset consisting of free target structures, co-crystallized template complexes with sequence identify with respect to the targets as low as 44%, and experimental ΔΔG measurements. We obtain similar results by fitting to a low-resolution Cryo-EM density map. Results suggest that other structural constraints may lead to a similar outcome, making the method even more broadly applicable.

MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory.

Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as viruses and ribosomes. Dynamical simulation codes enable modeling of conformational changes, but may require considerable time and many CPUs. There is an unmet demand from structural and molecular biologists for software in the middle ground, which would allow visualization combined with quick and interactive modeling of conformational changes, even of large complexes. This motivates MMB-GUI. MMB uses an internal-coordinate, multiscale approach, yielding as much as a 2000-fold speedup over conventional simulation methods. We use Chimera as an interactive graphical interface to control MMB. We show how this can be used for morphing of macromolecules that can be heterogeneous in biopolymer type, sequence, and chain count, accurately recapitulating structural intermediates. We use MMB-GUI to create a possible trajectory of EF-G mediated gate-passing translocation in the ribosome, with all-atom structures. This shows that the GUI makes modeling of large macromolecules accessible to a wide audience. The morph highlights similarities in tRNA conformational changes as tRNA translocates from A to P and from P to E sites and suggests that tRNA flexibility is critical for translocation completion.

A conserved histidine in switch-II of EF-G moderates release of inorganic phosphate.

Elongation factor G (EF-G), a translational GTPase responsible for tRNA-mRNA translocation possesses a conserved histidine (H91 in Escherichia coli) at the apex of switch-II, which has been implicated in GTPase activation and GTP hydrolysis. While H91A, H91R and H91E mutants showed different degrees of defect in ribosome associated GTP hydrolysis, H91Q behaved like the WT. However, all these mutants, including H91Q, are much more defective in inorganic phosphate (Pi) release, thereby suggesting that H91 facilitates Pi release. In crystal structures of the ribosome bound EF-G•GTP a tight coupling between H91 and the γ-phosphate of GTP can be seen. Following GTP hydrolysis, H91 flips ~140° in the opposite direction, probably with Pi still coupled to it. This, we suggest, promotes Pi to detach from GDP and reach the inter-domain space of EF-G, which constitutes an exit path for the Pi. Molecular dynamics simulations are consistent with this hypothesis and demonstrate a vital role of an Mg(2+) ion in the process.

Structural and Functional Impact of Parkinson Disease-Associated Mutations in the E3 Ubiquitin Ligase Parkin.

Mutations in the PARKIN/PARK2 gene that result in loss-of-function of the encoded, neuroprotective E3 ubiquitin ligase Parkin cause recessive, familial early-onset Parkinson disease. As an increasing number of rare Parkin sequence variants with unclear pathogenicity are identified, structure-function analyses will be critical to determine their disease relevance. Depending on the specific amino acids affected, several distinct pathomechanisms can result in loss of Parkin function. These include disruption of overall Parkin folding, decreased solubility, and protein aggregation. However pathogenic effects can also result from misregulation of Parkin autoinhibition and of its enzymatic functions. In addition, interference of binding to coenzymes, substrates, and adaptor proteins can affect its catalytic activity too. Herein, we have performed a comprehensive structural and functional analysis of 21 PARK2 missense mutations distributed across the individual protein domains. Using this combined approach, we were able to pinpoint some of the pathogenic mechanisms of individual sequence variants. Similar analyses will be critical in gaining a complete understanding of the complex regulations and enzymatic functions of Parkin. These studies will not only highlight the important residues, but will also help to develop novel therapeutics aimed at activating and preserving an active, neuroprotective form of Parkin.

Cysteines in the neuropilin-2 MAM domain modulate receptor homooligomerization and signal transduction.

Neuropilins (NRPs) are transmembrane receptors involved in angiogenesis, lymphangiogenesis, and neuronal development as well as in cancer metastasis. Previous studies suggest that NRPs exist in heteromeric complexes with vascular endothelial growth factors (VEGFs) and VEGF receptors as well as plexins and semaphorins. We determined via site-directed mutagenesis and bioluminescent resonance energy transfer assays that a conserved cysteine (C711) in the Danio rerio NRP2a MAM (meprin, A-5 protein, and protein tyrosine phosphatase µ) domain modulates NRP2a homomeric interactions. Mutation of this residue also disrupts semaphorin-3F binding in NRP2a-transfected COS-7 cells and prevents the NRP2a overexpression effects in a zebrafish vascular model. Collectively, our results indicate the MAM domain plays an important role in defining the NRP2 homodimer structure, which is important for semaphorin-dependent signal transduction via NRP2.

Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin.

Loss-of-function mutations in PINK1 or PARKIN are the most common causes of autosomal recessive Parkinson's disease. Both gene products, the Ser/Thr kinase PINK1 and the E3 Ubiquitin ligase Parkin, functionally cooperate in a mitochondrial quality control pathway. Upon stress, PINK1 activates Parkin and enables its translocation to and ubiquitination of damaged mitochondria to facilitate their clearance from the cell. Though PINK1-dependent phosphorylation of Ser65 is an important initial step, the molecular mechanisms underlying the activation of Parkin's enzymatic functions remain unclear. Using molecular modeling, we generated a complete structural model of human Parkin at all atom resolution. At steady state, the Ub ligase is maintained inactive in a closed, auto-inhibited conformation that results from intra-molecular interactions. Evidently, Parkin has to undergo major structural rearrangements in order to unleash its catalytic activity. As a spark, we have modeled PINK1-dependent Ser65 phosphorylation in silico and provide the first molecular dynamics simulation of Parkin conformations along a sequential unfolding pathway that could release its intertwined domains and enable its catalytic activity. We combined free (unbiased) molecular dynamics simulation, Monte Carlo algorithms, and minimal-biasing methods with cell-based high content imaging and biochemical assays. Phosphorylation of Ser65 results in widening of a newly defined cleft and dissociation of the regulatory N-terminal UBL domain. This motion propagates through further opening conformations that allow binding of an Ub-loaded E2 co-enzyme. Subsequent spatial reorientation of the catalytic centers of both enzymes might facilitate the transfer of the Ub moiety to charge Parkin. Our structure-function study provides the basis to elucidate regulatory mechanisms and activity of the neuroprotective Parkin. This may open up new avenues for the development of small molecule Parkin activators through targeted drug design.

Obesity and pro-inflammatory mediators are associated with acute kidney injury in patients with A/H1N1 influenza and acute respiratory distress syndrome.

BACKGROUND: The obesity has been shown to increase the severity of A/H1N1 infection and the development of acute respiratory distress syndrome (ARDS) and organ involvement. METHODS: Circulating levels of C-peptide, insulin, glucagon, leptin, acute phase reactants (procalcitonin, C-reactive protein, tissue plasminogen activator, and serum amyloids A and P), were measured in samples from 32 critically ill patients with A/H1N1 virus infection, 17 of whom had ARDS complicated by acute kidney injury (AKI) and 15 of whom had ARDS but did not develop AKI. RESULTS: Patients with ARDS and AKI (ARDS/AKI) had higher BMI and higher levels of C-peptide, insulin, leptin, procalcitonin and serum amyloid A compared to those ARDS patient who did not develop AKI. Adjusting for confounding variables using logistic regression analysis, higher levels of C-peptide (>0.75 ng/mL) (OR=64.8, 95% CI = 2.1-1980, p = 0.0006) and BMI>30 Kg/m(2) (OR = 42.0, 95% CI = 1.2-1478, p = 0.04) were significantly associated with the development of AKI in ARDS patients. CONCLUSION: High levels of C-peptide and BMI>30 kg/m(2) were associated with the development of AKI in ARDS patients due to A/H1N1 infection. These metabolic/obesity indicators, together with the profiles of pro-inflammatory acute phase proteins, may be important links between obesity and poor outcomes in A/H1N1 09 infection.

A multiscale approach to predicting affinity changes in protein-protein interfaces.

Substitution mutations in protein-protein interfaces can have a substantial effect on binding, which has consequences in basic and applied biomedical research. Experimental expression, purification, and affinity determination of protein complexes is an expensive and time-consuming means of evaluating the effect of mutations, making a fast and accurate in silico method highly desirable. When the structure of the wild-type complex is known, it is possible to economically evaluate the effect of point mutations with knowledge based potentials, which do not model backbone flexibility, but these have been validated only for single mutants. Substitution mutations tend to induce local conformational rearrangements only. Accordingly, ZEMu (Zone Equilibration of Mutants) flexibilizes only a small region around the site of mutation, then computes its dynamics under a physics-based force field. We validate with 1254 experimental mutants (with 1-15 simultaneous substitutions) in a wide variety of different protein environments (65 protein complexes), and obtain a significant improvement in the accuracy of predicted ΔΔG.

Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome.

Determining the conformational rearrangements of large macromolecules is challenging experimentally and computationally. Case in point is the ribosome; it has been observed by high-resolution crystallography in several states, but many others are known only from low-resolution methods including cryo-electron microscopy. Combining these data into dynamical trajectories that may aid understanding of its largest-scale conformational changes has so far remained out of reach of computational methods. Most existing methods either model all atoms explicitly, resulting in often prohibitive cost, or use approximations that lose interesting structural and dynamical detail. In this work, I introduce Internal Coordinate Flexible Fitting, which uses full atomic forces and flexibility in limited regions of a model, capturing extensive conformational rearrangements at low cost. I use it to turn multiple low-resolution density maps, crystallographic structures and biochemical information into unified all-atoms trajectories of ribosomal translocation. Internal Coordinate Flexible Fitting is three orders of magnitude faster than the most comparable existing method.

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies.

Insights into diseases of human telomerase from dynamical modeling.

Mutations in the telomerase complex disrupt either nucleic acid binding or catalysis, and are the cause of numerous human diseases. Despite its importance, the structure of the human telomerase complex has not been observed crystallographically, nor are its dynamics understood in detail. Fragments of this complex from Tetrahymena thermophila and Tribolium castaneum have been crystallized. Biochemical probes provide important insight into dynamics. In this work we summarize evidence that the T. castaneum structure is Telomerase Reverse Transcriptase. We use this structure to build a partial model of the human Telomerase complex. The model suggests an explanation for the structural role of several disease-associated mutations. We then generate a 3D kinematic trajectory of telomere elongation to illustrate a "typewriter" mechanism: the RNA template moves to keep the end of the growing telomeric primer in the active site, disengaging after every 6-residue extension to execute a "carriage return" and go back to its starting position. A hairpin can easily form in the primer, from DNA residues leaving the primer-template duplex. The trajectory is consistent with available experimental evidence. The methodology is extensible to many problems in structural biology in general and personalized medicine in particular.