Synergistic increase in coproporphyrin III biosynthesis by mitochondrial compartmentalization in engineered Saccharomyces cerevisiae.

Coproporphyrin III (CP III), a natural porphyrin derivative, has extensive applications in the biomedical and material industries. S. cerevisiae has previously been engineered to highly accumulate the CP III precursor 5-aminolevulinic acid (ALA) through the C4 pathway. In this study, a combination of cytoplasmic metabolic engineering and mitochondrial compartmentalization was used to enhance CP III production in S. cerevisiae. By integrating pathway genes into the chromosome, the CP III titer gradually increased to 32.5 ± 0.5 mg/L in shake flask cultivation. Nevertheless, increasing the copy number of pathway genes did not consistently enhance CP III synthesis. Hence, the partial synthesis pathway was compartmentalized in mitochondria to evaluate its effectiveness in increasing CP III production. Subsequently, by superimposing the mitochondrial compartmentalization strategy on cytoplasmic metabolic engineered strains, the CP III titer was increased to 64.3 ± 1.9 mg/L. Furthermore, augmenting antioxidant pathway genes to reduce reactive oxygen species (ROS) levels effectively improved the growth of engineered strains, resulting in a further increase in the CP III titer to 82.9 ± 1.4 mg/L. Fed-batch fermentations in a 5 L bioreactor achieved a titer of 402.8 ± 9.3 mg/L for CP III. This study provides a new perspective on engineered yeast for the microbial production of porphyrins.

Linear integration of multisensory signals in the pupil.

The pupil of the eye responds to various salient signals from different modalities, but there is no consensus on how these pupillary responses are integrated when multiple signals appear simultaneously. Both linear and nonlinear integration have been found previously. The current study aimed to reexamine the nature of pupillary integration, and specifically focused on the early, transient pupillary responses due to its close relationship with orienting. To separate the early pupillary responses out of the pupil time series, we adopted a pupil oscillation paradigm in which sensory stimuli were periodically presented. The simulation analysis confirmed that the amplitude of the pupil oscillation, induced by stimuli repeatedly presented at relatively high rates, can precisely reflect the early, transient pupillary responses without involving the late and sustained pupillary responses. The experimental results then showed that the amplitude of pupil oscillation induced by a series of simultaneous audiovisual stimuli equaled to a linear summation of the oscillatory amplitudes when unisensory stimuli were presented alone. Moreover, the tonic arousal levels, indicated by the baseline pupil size, cannot shift the summation from linear to nonlinear. These findings together support the additive nature of multisensory pupillary integration for the early, orienting-related pupillary responses. The additive nature of pupillary integration further implies that multiple pupillary responses may be independent of each other, irrespective of their potential cognitive and neural drivers.

Eye pupil signals life motion perception.

The ability to readily detect and recognize biological motion (BM) is fundamental to survival and interpersonal communication. However, perception of BM is strongly disrupted when it is shown upside down. This well-known inversion effect is proposed to be caused by a life motion detection mechanism highly tuned to gravity-compatible motion cues. In the current study, we assessed the inversion effect in BM perception using a no-report pupillometry. We found that the pupil size was significantly enlarged when observers viewed upright BMs (gravity-compatible) compared with the inverted counterparts (gravity-incompatible). Importantly, such an effect critically depended on the dynamic biological characteristics, and could be extended to local feet motion signals. These findings demonstrate that the eye pupil can signal gravity-dependent life motion perception. More importantly, with the convenience, objectivity, and noninvasiveness of pupillometry, the current study paves the way for the potential application of pupillary responses in detecting the deficiency of life motion perception in individuals with socio-cognitive disorders.

Looking more masculine among females: Spatial context modulates gender perception of face and biological motion.

Perception of visual information highly depends on spatial context. For instance, perception of a low-level visual feature, such as orientation, can be shifted away from its surrounding context, exhibiting a simultaneous contrast effect. Although previous studies have demonstrated the adaptation aftereffect of gender, a high-level visual feature, it remains largely unknown whether gender perception can also be shaped by a simultaneously presented context. In the present study, we found that the gender perception of a central face or a point-light walker was repelled away from the gender of its surrounding faces or walkers. A norm-based opponent model of lateral inhibition, which accounts for the adaptation aftereffect of high-level features, can also excellently fit the simultaneous contrast effect. But different from the reported contextual effect of low-level features, the simultaneous contrast effect of gender cannot be observed when the centre and the surrounding stimuli are from different categories, or when the surrounding stimuli are suppressed from awareness. These findings on one hand reveal a resemblance between the simultaneous contrast effect and the adaptation aftereffect of high-level features, on the other hand highlight different biological mechanisms underlying the contextual effects of low- and high-level visual features.

Metformin promotes smear conversion in tuberculosis-diabetes comorbidity and construction of prediction models.

BACKGROUND: The comorbidity of tuberculosis (TB) and diabetes mellitus (DM) is a global health concern. Metformin is commonly used in DM but the potential effectiveness in comorbid patients is uncertain. This retrospective study aims to investigate the effect of metformin on TB-DM comorbidity and construct prediction models. METHODS: Patients diagnosed with TB-DM in West China Hospital were retrospectively enrolled from Nov 2013 to Sep 2019. Electronic health records of patients were extracted. Two-month smear conversion (2SC) was considered an outcome indicator of TB. Univariate and multivariate logistic regression (LR) were used to assess the role of metformin and other independent predictors. Meanwhile, prediction models were built by LR, elastic net regression, support vector machine, k-nearest neighbors, and random forest. RESULTS: A total of 927 individuals were recruited, among which 408 (44.01%) were metformin-exposed patients. A higher 2SC rate was observed in the metformin users. Other impact factors such as smoking, glucose, and creatinine levels were also identified. Multivariable models were then constructed using filtered variables. The support vector machine model yields the highest AUC (0.808, 95% CI: 0.767-0.849) and specificity (83.24%). LR model outperformed others in terms of sensitivity (69.71%). CONCLUSION: This retrospective study of a large population from southwestern China provides strong clinical evidence for the positive effects of metformin in TB-DM. Metformin is associated with a better therapeutic outcome and promising for the adjuvant therapy of TB-DM. Furthermore, a combination of support vector machine and LR models is recommended to discriminate the patients with poor treatment outcomes.

Exploring the eligibility of all reported lipoarabinomannan-testing assays in different clinical situations: a systematic review and meta-analysis of 97 articles.

OBJECTIVES: How to choose proper lipoarabinomannan-testing assays for diagnosing tuberculosis (TB) in different populations baffles clinicians. This work assessed all reported lipoarabinomannan assays' performance and aimed to identify the eligibility of each assay and offer guidance for clinicians. METHODS: We searched PubMed, Embase, and Web of Science until August 23, 2020. The risk of bias was evaluated by QADAS-2. Heterogeneity was evaluated by the Cochran Q test and I2. Sensitivity and specificity were pooled by a bivariate mixed model (register number: CRD42021270506). RESULTS: A total of 97 articles, covering 144 trials, 16 assays, 45,679 participants, and eight sample types, were divided into five groups. Electrochemiluminescence (ECL) had a sensitivity of 65%, specificity of 92%, and an area under curve (AUC) of 0.85 in diagnosing pulmonary TB in adults. ECL showed a promising diagnostic ability (sensitivity: 78%; specificity: 88%; AUC: 0.88) in patients with HIV, especially for urine detection (sensitivity: 90%; specificity: 89%; AUC: 0.95). The enzyme-linked immune assay showed a preference for diagnosing TB in Asians and Africans, especially in Africans who were smear-positive (sensitivity: 80%; specificity: 88%; AUC: 0.91). CONCLUSION: ECL was recommended for diagnosing pulmonary TB in adults, especially for TB/HIV co-infection. Taking urine as a sample further enhanced ECL's diagnostic performance. Enzyme-linked immune assay was recommended as an additional TB-related detection for smear-positive Africans.

Following Other People's Footsteps: A Contextual-Attraction Effect Induced by Biological Motion.

Our visual system is bombarded with numerous social interactions that form intangible social bonds among people, as exemplified by synchronized walking in crowds. Here, we investigated whether these perceived social bonds implicitly intrude on visual perception and induce a contextual effect. Using multiple point-light walkers and a classical contextual paradigm, we tested 72 college-age adults across six experiments and found that the perceived direction of the central walker was attracted toward the direction of the surrounding walkers. The observed contextual-attraction effect occurred even when the surrounding walkers differed from the central walker in gender and walking speed but disappeared when they were asynchronously presented or replaced by inanimate motion. Strikingly, this contextual-attraction effect partially persisted in the context of local motion rather than static figures. These findings, in contrast to the typical contextual-repulsion effect, lend support for the distinctiveness of perceived social bonds on contextual modulation and suggest a specialized contextual mechanism tuned to social factors.

Multisensory signals inhibit pupillary light reflex: Evidence from pupil oscillation.

Multisensory integration, which enhances stimulus saliency at the early stage of the processing hierarchy, has been recently shown to produce a larger pupil size than its unisensory constituents. Theoretically, any modulation on pupil size ought to be associated with the sympathetic and parasympathetic pathways that are sensitive to light. But it remains poorly understood how the pupillary light reflex is changed in a multisensory context. The present study evoked an oscillation of the pupillary light reflex by periodically changing the luminance of a visual stimulus at 1.25 Hz. It was found that such induced pupil size oscillation was substantially attenuated when the bright but not the dark phase of the visual flicker was periodically and synchronously presented with a burst of tones. This inhibition effect persisted when the visual flicker was task-irrelevant and out of attentional focus, but disappeared when the visual flicker was moved from the central field to the periphery. These findings not only offer a comprehensive characterization of the multisensory impact on pupil response to light, but also provide valuable clues about the individual contributions of the sympathetic and parasympathetic pathways to multisensory modulation of pupil size.

Collagen type XVIII alpha 1 chain (COL18A1) variants affect the risk of anti-tuberculosis drug-induced hepatotoxicity: A prospective study.

BACKGROUND: The role of collagen type XVIII alpha 1 chain (COL18A1) in anti-tuberculosis drug-induced hepatotoxicity (ATDH) has not been reported. This study aimed to explore the association between of COL18A1 variants and ATDH susceptibility. METHODS: A total of 746 patients were enrolled in our study from December 2016 to April 2018, and all subjects in the study signed an informed consent form. The custom-by-design 2x48-Plex SNPscanTM kit was used to genotype all selected 11 SNPs. Categorical variables were compared by chi-square (χ2 ) or Fisher's exact test, while continuous variables were compared by Mann-Whitney's U test. Plink was utilized to analyze allelic and genotypic frequencies, and genetic models. Multivariate logistic regression analyses were used to adjust potential factors. The odds ratios (ORs) with corresponding 95% confidence intervals (CIs) were also calculated. RESULTS: Among patients with successfully genotyping, there were 114 cases and 612 controls. The mutant A allele of rs12483377 conferred the decreased risk of ATDH (OR = 0.13, 95%CI: 0.02-0.98, P = 0.020), and this significance still existed after adjusting age and gender (P = 0.024). The mutant homozygote AA genotype of rs12483377 was associated with decreased total protein levels (P = 0.018). CONCLUSION: Our study first revealed that the A allele of COL18A1 rs12483377 was associated with the decreased risk of ATDH in the Western Chinese Han population, providing new perspective for the molecular prediction, precise diagnosis, and individual treatment of ATDH.

Systematic evaluation, verification and comparison of tuberculosis-related non-coding RNA diagnostic panels.

We systematically summarized tuberculosis (TB)-related non-coding RNA (ncRNA) diagnostic panels, validated and compared panel performance. We searched TB-related ncRNA panels in PubMed, OVID and Web of Science up to 28 February 2020, and available datasets in GEO, SRA and EBI ArrayExpress up to 1 March 2020. We rebuilt models and synthesized the results of each model in validation sets by bivariate mixed models. Specificity at 90% sensitivity, area under curve (AUC) and inconsistence index (I2 ) were calculated. NcRNA biofunctions were analysed. Nineteen models based on 18 ncRNA panels (miRNA, lncRNA, circRNA and snoRNA panels) and 18 datasets were included. Limited available datasets only allowed to evaluate miRNA panels further. Cui 2017 and Latorre 2015 exhibited specificity >70% at 90% sensitivity and AUC >80% in all validation sets. Cui 2017 showed higher specificity at 90% sensitivity (92%) and AUC (95%) and lower heterogeneity (I2  = 0%) in ethological-confirmation validation sets. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that most ncRNAs in panels involved in immune cell activation, oxidative stress, and Wnt and MAPK signalling pathway. Cui 2017 outperformed other models in both all available and aetiological-confirmed validation sets, meeting the criteria of target product profile of WHO. This work provided a basis for clinical choice of TB-related ncRNA diagnostic panels to a certain extent.

Which sample type is better for Xpert MTB/RIF to diagnose adult and pediatric pulmonary tuberculosis?

OBJECTIVE: This review aimed to identify proper respiratory-related sample types for adult and pediatric pulmonary tuberculosis (PTB), respectively, by comparing performance of Xpert MTB/RIF when using bronchoalveolar lavage (BAL), induced sputum (IS), expectorated sputum (ES), nasopharyngeal aspirates (NPAs), and gastric aspiration (GA) as sample. METHODS: Articles were searched in Web of Science, PubMed, and Ovid from inception up to 29 June 2020. Pooled sensitivity and specificity were calculated, each with a 95% confidence interval (CI). Quality assessment and heterogeneity evaluation across included studies were performed. RESULTS: A total of 50 articles were included. The respective sensitivity and specificity were 87% (95% CI: 0.84-0.89), 91% (95% CI: 0.90-0.92) and 95% (95% CI: 0.93-0.97) in the adult BAL group; 90% (95% CI: 0.88-0.91), 98% (95% CI: 0.97-0.98) and 97% (95% CI: 0.95-0.99) in the adult ES group; 86% (95% CI: 0.84-0.89) and 97% (95% CI: 0.96-0.98) in the adult IS group. Xpert MTB/RIF showed the sensitivity and specificity of 14% (95% CI: 0.10-0.19) and 99% (95% CI: 0.97-1.00) in the pediatric ES group; 80% (95% CI: 0.72-0.87) and 94% (95% CI: 0.92-0.95) in the pediatric GA group; 67% (95% CI: 0.62-0.72) and 99% (95% CI: 0.98-0.99) in the pediatric IS group; and 54% (95% CI: 0.43-0.64) and 99% (95% CI: 0.97-0.99) in the pediatric NPA group. The heterogeneity across included studies was deemed acceptable. CONCLUSION: Considering diagnostic accuracy, cost and sampling process, ES was a better choice than other sample types for diagnosing adult PTB, especially HIV-associated PTB. GA might be more suitable than other sample types for diagnosing pediatric PTB. The actual choice of sample types should also consider the needs of specific situations.

Comparison of the clinical benefits for non-small cell lung cancer patients between different volume of pleural lavage fluid following video-assisted thoracoscopic lobectomy and systematic mediastinal lymph node dissection: study protocol for a randomized controlled trial.

BACKGROUND: Pleural lavage is regularly performed before closing the chest wall in pulmonary surgeries to prevent pleural implantation of tumor cells and postoperative infection. However, scant data could be found in the literature regarding the optimal regimen for performing pleural lavage. To establish a proper volume of pleural lavage, we herein designed a protocol for a randomized controlled trial. METHODS: A total of 400 participants with non-small cell lung cancer undergoing video-assisted thoracoscopic surgery (VATS) lobectomy and systematic mediastinal lymph node dissection (MLND) will be randomly assigned to one of two groups: group A (500 mL pleural lavage fluid) and group B (3000 mL pleural lavage fluid). The primary outcomes include the levels of leukocytes, neutrophils, and inflammatory factors on the first postoperative day. The secondary outcomes include (i) the levels of leukocytes, neutrophils, and inflammatory factors on the second and third postoperative days; (ii) the incidence of postoperative fever on the first, second, and third postoperative days; (iii) the volumes of chest drainage within the first 3 operative days, the duration of drainage, and postoperative hospitalization; and (iv) the incidence of postoperative complications (incision infection, pain, atelectasis, hemorrhage, etc.) and the incidence of pleural effusion requiring thoracic puncture or drainage within 30 days after surgery. The main content of the analysis includes effectiveness and safety analysis. We will perform subgroup analyses to identify potential influence factors. DISCUSSION: As far as we know, this will be the first randomized controlled trial to compare the clinical outcomes between different volumes of pleural lavage fluid following VATS and MLND. Findings from this trial will determine the appropriate amount of pleural lavage before chest wall closure. TRIAL REGISTRATION: This study was registered with the Chinese Clinical Trial Registry ( on 17 March 2019. ChiCTR 1900021950).

The genetic variants in calcium signaling related genes influence anti-tuberculosis drug induced liver injury: A prospective study.

Although many genetic variants related to anti-tuberculosis drug induced liver injury (ATDILI) have been identified, the prediction and personalized treatment of ATDILI have failed to achieve, indicating there remains an area for further exploration. This study aimed to explore the influence of single nucleotide polymorphisms (SNPs) in Bradykinin receptor B2 (BDKRB2), Teneurin transmembrane protein 2 (TENM2), transforming growth factor beta 2 (TGFB2), and solute carrier family 2 member 13 (SLC2A13) on the risk of ATDILI.The subjects comprised 746 Chinese tuberculosis (TB) patients. Custom-by-design 2x48-Plex SNPscanTM kit was employed to genotype 28 selected SNPs. The associations of SNPs with ATDILI risk and clinical phenotypes were analyzed according to the distributions of allelic and genotypic frequencies and different genetic models. The odds ratio (OR) with corresponding 95% confidence interval (CI) was calculated.Among subjects with successfully genotyped, 107 participants suffered from ATDILI during follow-up. In BDKRB2, patients with rs79280755 G allele or rs117806152 C allele were more vulnerable to ATDILI (PBonferronicorrection = .002 and .03, respectively). Rs79280755 increased the risk of ATDILI significantly whether in additive (OR = 3.218, 95% CI: 1.686-6.139, PBonferroni correction = .003) or dominant model (PBonferroni correction = .003), as well as rs117806152 (Additive model: PBonferroni correction = .05; dominant model: PBonferroni correction = .03). For TENM2, rs80003210 G allele contributed to the decreased risk of ATDILI (PBonferroni correction = .02), while rs2617972 A allele conferred susceptibility to ATDILI (PBonferroni correction = .01). Regarding rs2617972, significant findings were also observed in both additive (OR = 3.203, 95% CI: 1.487-6.896, PBonferroni correction = .02) and dominant model (PBonferroni correction = .02). Moreover, rs79280755 and rs117806152 in BDKRB2 significantly affected some laboratory indicators. However, no meaningful SNPs were observed in TGFB2 and SLC2A13.Our study revealed that both BDKRB2 and TENM2 genetic polymorphisms were interrogated in relation to ATDILI susceptibility and some laboratory indicators in the Western Chinese Han population, shedding a new light on exploring novel biomarkers and targets for ATDILI.

Identification and characterization of proteins with phenoloxidase-like activities in the sea urchin Strongylocentrotus nudus.

Three proteins with PO-like activities in the coelomocytes of sea urchin Strongylocentrotus nudus were identified using electrophoretic method and named as SnPO1, SnPO2 and SnPO3 according to their molecular mass from high to low. The SnPOs were characterized for substrate specificity and the effects of temperature, pH, divalent metal ions and inhibitors on PO activities. They showed oxidative activities to L-3,4-dihydroxyphenylalanine. (l-DOPA), dopamine and hydroquinone, but failed to oxidize tyrosine, which illustrated the three proteins had laccase-like PO activities. The optimum temperature for the activities of SnPO1, SnPO2 and SnPO3 was 75 °C, 70 °C, 40 °C, and the optimum pH was 7.0, 9.0, 8.0, respectively. The SnPOs were notably activated after being incubated in boiled water for 60 min, suggesting that the three proteins are thermophilic. The activity of SnPO1 was greatly enhanced by Cu(2+), Mn(2+) and Fe(2+) and inhibited by Pb(2+), Cd(2+), EDTA, DETC, sodium sulfite and ascorbic acid, but SnPO2 and SnPO3 were not obviously affected by Pb(2+) and Cd(2+), suggesting the three proteins are copper-containing, and the catalytic properties of SnPO1 might be different from those of SnPO2 and SnPO3. Taken together, SnPO1, SnPO2 and SnPO3 might play different roles in the immune and physiological processes of S. nudus.

Molecular dynamics study of the proposed proton transport pathways in [FeFe]-hydrogenase.

Possible proton transport pathways in Clostridium pasteurianum (CpI) [FeFe]-hydrogenase were investigated with molecular dynamics simulations. This study was undertaken to evaluate the functional pathway and provide insight into the hydrogen bonding features defining an active proton transport pathway. Three pathways were evaluated, two of which consist of water wires and one of predominantly amino acid residues. Our simulations suggest that protons are not transported through water wires. Instead, the five-residue motif (Glu282, Ser319, Glu279, H2O, Cys299) was found to be the likely pathway, consistent with previously made experimental observations. The pathway was found to have a persistent hydrogen bonded core (residues Cys299 to Ser319), with less persistent hydrogen bonds at the ends of the pathway for both H2 release and H2 uptake. Single site mutations of the four residues have been shown experimentally to deactivate the enzyme. The theoretical evaluation of these mutations demonstrates redistribution of the hydrogen bonds in the pathway, resulting in enzyme deactivation. Finally, coupling between the protein dynamics near the proton transport pathway and the redox partner binding regions was also found as a function of H2 uptake and H2 release states, which may be indicative of a correlation between proton and electron movement within the enzyme.

Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes.

Multi-scale modeling plays an important role in understanding the structure and biological functionalities of large biomolecular complexes. In this paper, we present an efficient computational framework to construct multi-scale models from atomic resolution data in the Protein Data Bank (PDB), which is accelerated by multi-core CPU and programmable Graphics Processing Units (GPU). A multi-level summation of Gaus-sian kernel functions is employed to generate implicit models for biomolecules. The coefficients in the summation are designed as functions of the structure indices, which specify the structures at a certain level and enable a local resolution control on the biomolecular surface. A method called neighboring search is adopted to locate the grid points close to the expected biomolecular surface, and reduce the number of grids to be analyzed. For a specific grid point, a KD-tree or bounding volume hierarchy is applied to search for the atoms contributing to its density computation, and faraway atoms are ignored due to the decay of Gaussian kernel functions. In addition to density map construction, three modes are also employed and compared during mesh generation and quality improvement to generate high quality tetrahedral meshes: CPU sequential, multi-core CPU parallel and GPU parallel. We have applied our algorithm to several large proteins and obtained good results.

Development of in vitro models to demonstrate the ability of PecSys®, an in situ nasal gelling technology, to reduce nasal run-off and drip.

UNLABELLED: Many of the increasing number of intranasal products available for either local or systemic action can be considered sub-optimal, most notably where nasal drip or run-off give rise to discomfort/tolerability issues or reduced/variable efficacy. PecSys, an in situ gelling technology, contains low methoxy (LM) pectin which gels due to interaction with calcium ions present in nasal fluid. PecSys is designed to spray readily, only forming a gel on contact with the mucosal surface. The present study employed two in vitro models to confirm that gelling translates into a reduced potential for drip/run-off: (i) Using an inclined TLC plate treated with a simulated nasal electrolyte solution (SNES), mean drip length [±SD, n = 10] was consistently much shorter for PecSys (1.5 ± 0.4 cm) than non-gelling control (5.8 ± 1.6 cm); (ii) When PecSys was sprayed into a human nasal cavity cast model coated with a substrate containing a physiologically relevant concentration of calcium, PecSys solution was retained at the site of initial deposition with minimal redistribution, and no evidence of run-off/drip anteriorly or down the throat. In contrast, non-gelling control was significantly more mobile and consistently redistributed with run-off towards the throat. CONCLUSION: In both models PecSys significantly reduced the potential for run-off/drip ensuring that more solution remained at the deposition site. In vivo, this enhancement of retention will provide optimum patient acceptability, modulate drug absorption and maximize the ability of drugs to be absorbed across the nasal mucosa and thus reduce variability in drug delivery.

Modeling effects of L-type ca(2+) current and na(+)-ca(2+) exchanger on ca(2+) trigger flux in rabbit myocytes with realistic T-tubule geometries.

The transverse tubular system of rabbit ventricular myocytes consists of cell membrane invaginations (t-tubules) that are essential for efficient cardiac excitation-contraction coupling. In this study, we investigate how t-tubule micro-anatomy, L-type Ca(2+) channel (LCC) clustering, and allosteric activation of Na(+)/Ca(2+) exchanger by L-type Ca(2+) current affects intracellular Ca(2+) dynamics. Our model includes a realistic 3D geometry of a single t-tubule and its surrounding half-sarcomeres for rabbit ventricular myocytes. The effects of spatially distributed membrane ion-transporters (LCC, Na(+)/Ca(2+) exchanger, sarcolemmal Ca(2+) pump, and sarcolemmal Ca(2+) leak), and stationary and mobile Ca(2+) buffers (troponin C, ATP, calmodulin, and Fluo-3) are also considered. We used a coupled reaction-diffusion system to describe the spatio-temporal concentration profiles of free and buffered intracellular Ca(2+). We obtained parameters from voltage-clamp protocols of L-type Ca(2+) current and line-scan recordings of Ca(2+) concentration profiles in rabbit cells, in which the sarcoplasmic reticulum is disabled. Our model results agree with experimental measurements of global Ca(2+) transient in myocytes loaded with 50 µM Fluo-3. We found that local Ca(2+) concentrations within the cytosol and sub-sarcolemma, as well as the local trigger fluxes of Ca(2+) crossing the cell membrane, are sensitive to details of t-tubule micro-structure and membrane Ca(2+) flux distribution. The model additionally predicts that local Ca(2+) trigger fluxes are at least threefold to eightfold higher than the whole-cell Ca(2+) trigger flux. We found also that the activation of allosteric Ca(2+)-binding sites on the Na(+)/Ca(2+) exchanger could provide a mechanism for regulating global and local Ca(2+) trigger fluxes in vivo. Our studies indicate that improved structural and functional models could improve our understanding of the contributions of L-type and Na(+)/Ca(2+) exchanger fluxes to intracellular Ca(2+) dynamics.

Gating and Intermolecular Interactions in Ligand-Protein Association: Coarse-Grained Modeling of HIV-1 Protease.

Most biological processes are initiated or mediated by the association of ligands and proteins. This work studies multistep, ligand-protein association processes by Brownian dynamics simulations with coarse-grained models for HIV-1 protease (HIVp) and its neutral ligands. We report the average association times when the ligand concentration is 100 µM. The influence of crowding on the simulated binding time was also studied. HIVp has flexible loops that serve as a gate during the ligand binding processes. It is believed that the flaps are partially closed most of the time in its free state. To accelerate our simulations, we fixed a part of the HIVp and reparameterized our coarse-grained model, using atomistic molecular dynamics simulations, to reproduce the "gating" motions of HIVp. HIVp-ligand interactions changed the gating behavior of HIVp and helped ligands diffuse on HIVp surface to accelerate binding. The structural adjustment of the ligand toward its final stable state was the limiting step in the binding processes, which is highly system dependent. The intermolecular attraction between the ligands and crowder proteins contributes the most to the crowding effects. The results highlight broader implications in recognition pathways under more complex environment that considers molecular dynamics and conformational changes. This work brings insights into ligand-protein associations and is helpful in the design of targeted ligands.