Coarse‐grained and all‐atom modeling of structural states and transitions in hemoglobin

Hemoglobin (Hb), an oxygen‐binding protein composed of four subunits (α1, α2, β1, and β2), is a well‐known example of allosteric proteins that are capable of cooperative ligand binding. Despite decades of studies, the structural basis of its cooperativity remains controversial. In this study, we have integrated coarse‐grained (CG) modeling, all‐atom simulation, and structural data from X‐ray crystallography and wide‐angle X‐ray scattering (WAXS), aiming to probe dynamic properties of the two structural states of Hb (T and R state) and the transitions between them. First, by analyzing the WAXS data of unliganded and liganded Hb, we have found that the structural ensemble of T or R state is dominated by one crystal structure of Hb with small contributions from other crystal structures of Hb. Second, we have used normal mode analysis to identify two distinct quaternary rotations between the α1β1 and α2β2 dimer, which drive the transitions between T and R state. We have also identified the hot‐spot residues whose mutations are predicted to greatly change these quaternary motions. Third, we have generated a CG transition pathway between T and R state, which predicts a clear order of quaternary and tertiary changes involving α and β subunits in Hb. Fourth, we have used the accelerated molecular dynamics to perform an all‐atom simulation starting from the T state of Hb, and we have observed a transition toward the R state of Hb. Further analysis of crystal structural data and the all‐atom simulation trajectory has corroborated the order of quaternary and tertiary changes predicted by CG modeling. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Alzheimer's disease amyloid-β peptide analogue alters the ps-dynamics of phospholipid membranes

We have investigated the influence of the neurotoxic Alzheimer's disease peptide amyloid-β (25-35) on the dynamics of phospholipid membranes by means of quasi-elastic neutron scattering in the picosecond time-scale. Samples of pure phospholipids (DMPC/DMPS) and samples with amyloid-β (25-35) peptide included have been compared. With two different orientations of the samples the directional dependence of the dynamics was probed. The sample temperature was varied between 290 K and 320 K to cover both the gel phase and the liquid-crystalline phase of the lipid membranes. The model for describing the dynamics combines a long-range translational diffusion of the lipid molecules and a spatially restricted diffusive motion. Amyloid-β (25-35) peptide affects significantly the ps-dynamics of oriented lipid membranes in different ways. It accelerates the lateral diffusion especially in the liquid-crystalline phase. This is very important for all kinds of protein-protein interactions which are enabled and strongly influenced by the lateral diffusion such as signal and energy transducing cascades. Amyloid-β (25-35) peptide also increases the local lipid mobility as probed by variations of the vibrational motions with a larger effect in the out-of-plane direction. Thus, the insertion of amyloid-β (25-35) peptide changes not only the structure of phospholipid membranes as previously demonstrated by us employing neutron diffraction (disordering effect on the mosaicity of the lipid bilayer system) but also the dynamics inside the membranes. The amyloid-β (25-35) peptide induced membrane alteration even at only 3 mol% might be involved in the pathology of Alzheimer's disease as well as be a clue in early diagnosis and therapy.     

Detection of early ischemic damage by analysis of mitochondrial function in skinned fibers

The skinned fibers technique was applied for studies of the effects of global acute ischemia (1 h at 37°C) and long time (15 h) hypothermic (4°C) preservation of isolated rat hearts under different conditions (immersion or low-flow perfusion) on mitochondrial function in the cells in vivo. Skinned fibers were obtained by using saponin for permeabilization of the sarcolemma in separated fiber bundles cut from left ventricle. The experimental protocol of the respiration rate determination included a cytochrome c test to check the intactness of the outer mitochondrial membrane. The apparent K_m for ADP and the effect of creatine on the mitochondrial activity were also evaluated in these permeabilized fibers, taken from different groups of hearts. The preservation of low-flow perfused hearts resulted only in a slight decrease of creatine (20 mM) stimulated respiration at 0.1 mM ADP. The fibers from ischemic hearts or from hearts preserved by immersion showed a decrease of the apparent K_m for ADP, and a complete loss of the stimulatory effect of creatine. In these fibers, we could observe that the outer mitochondrial membrane was damaged. In conclusion, the results of this study show that assessment of mitochondrial parameters sensitive to organelles swelling – intactness of outer membrane and functionally coupled creatine kinase reaction – are the most sensitive indicators of early hypoxic or ischemic damage to mitochondria. Their determination in biopsy samples could be used for evaluation of the efficiency of the cardiac protection in heart surgery. (Mol Cell Biochem 174: 79–85, 1997)     

A multi‐resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand‐binding site

In multi‐resolution simulations, different system components are simultaneously modeled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of ligand binding. Global properties of the rest of the protein also play an essential role, determining the structure and fluctuations of the binding site; however, these can be modeled on a coarser level. Similarly, in the most computationally efficient scheme only the solvent hydrating the active site requires atomistic detail. We present a methodology to couple atomistic and coarse‐grained protein models, while solvating the atomistic part of the protein in atomistic water. This allows a free choice of which protein and solvent degrees of freedom to include atomistically. This multi‐resolution methodology can successfully model stable ligand binding, and we further confirm its validity by exploring the reproduction of system properties relevant to enzymatic function. In addition to a computational speedup, such an approach can allow the identification of the essential degrees of freedom playing a role in a given process, potentially yielding new insights into biomolecular function. Proteins 2016; 84:1902–1913. © 2016 Wiley Periodicals, Inc.     

Detection of sequences in the cerebellar cortex: numerical estimate of the possible number of tidal-wave inducing sequences represented

The two major cortices of the brain--the cerebral and cerebellar cortex--are massively connected through intercalated nuclei (pontine, cerebellar and thalamic nuclei). We suggest that the two cortices co-operate by generating precise temporal patterns in the cerebral cortex that are detected in the cerebellar cortex as temporal patterns assembled spatially in the mossy fibers. We will begin by showing that the tidal-wave mechanism works in the cerebellar cortex as a read-out mechanism for such spatio-temporal patterns due to the synchronous activity they generate in the parallel fiber system which drives the Purkinje cells--the output neurons of the cerebellar cortex--to fire action potentials. We will review the anatomy of the mossy fibers and show that within a "beam", or "row" of cerebellar cortex the mossy fibers in principle could embed a vast number of tidal-wave generating sequences. Based on anatomical data we will argue that the cerebellar mossy fiber-granule cell-Purkinje cell system can potentially detect and--through learning--select from an enormous number of spatio-temporal patterns.     

Rac1 GTPase-deficient mouse lens exhibits defects in shape, suture formation, fiber cell migration and survival

Morphogenesis and shape of the ocular lens depend on epithelial cell elongation and differentiation into fiber cells, followed by the symmetric and compact organization of fiber cells within an enclosed extracellular matrix-enriched elastic capsule. The cellular mechanisms orchestrating these different events however, remain obscure. We investigated the role of the Rac1 GTPase in these processes by targeted deletion of expression using the conditional gene knockout (cKO) approach. Rac1 cKO mice were derived from two different Cre (Le-Cre and MLR-10) transgenic mice in which lens-specific Cre expression starts at embryonic day 8.75 and 10.5, respectively, in both the lens epithelium and fiber cells. The Le-Cre/Rac1 cKO mice exhibited an early-onset (E12.5) and severe lens phenotype compared to the MLR-10/Rac1 cKO (E15.5) mice. While the Le-Cre/Rac1 cKO lenses displayed delayed primary fiber cell elongation, lenses from both Rac1 cKO strains were characterized by abnormal shape, impaired secondary fiber cell migration, sutural defects and thinning of the posterior capsule which often led to rupture. Lens fiber cell N-cadherin/β-catenin/Rap1/Nectin-based cell–cell junction formation and WAVE-2/Abi-2/Nap1-regulated actin polymerization were impaired in the Rac1 deficient mice. Additionally, the Rac1 cKO lenses were characterized by a shortened epithelial sheet, reduced levels of extracellular matrix (ECM) proteins and increased apoptosis. Taken together, these data uncover the essential role of Rac1 GTPase activity in establishment and maintenance of lens shape, suture formation and capsule integrity, and in fiber cell migration, adhesion and survival, via regulation of actin cytoskeletal dynamics, cell adhesive interactions and ECM turnover.     

Superelastic Hybrid CNT/Graphene Fibers for Wearable Energy Storage

The demands for wearable technologies continue to grow and novel approaches for powering these devices are being enabled by the advent of new electromaterials and novel fabrication strategies. Herein, a novel approach is reported to develop superelastic wet‐spun hybrid carbon nanotube graphene fibers followed by electrodeposition of polyaniline to achieve a high‐performance fiber‐based supercapacitor. It is found that the specific capacitance of hybrid carbon nanotube (CNT)/graphene fiber is enhanced up to ≈39% using a graphene to CNT fiber ratio of 1:3. Fabrication of spring‐like coiled fiber coated with an elastic polymer shows an extraordinary elasticity capable of 800% strain while affording a specific capacitance of ≈138 F g^?1. The elastic rubber coating enables extreme stretchability and enabling cycles with up to 500% strain for thousands of cycles with no significant change in its performance. Multiple supercapacitors can be easily assembled in series or parallel to meet specific energy and power needs.     

Comparison of complex modeling strategies for prediction of a binary outcome based on a few,highly correlated predictors

Motivated by a clinical prediction problem, a simulation study was performed to compare different approaches for building risk prediction models. Robust prediction models for hospital survival in patients with acute heart failure were to be derived from three highly correlated blood parameters measured up to four times, with predictive ability having explicit priority over interpretability. Methods that relied only on the original predictors were compared with methods using an expanded predictor space including transformations and interactions. Predictors were simulated as transformations and combinations of multivariate normal variables which were fitted to the partly skewed and bimodally distributed original data in such a way that the simulated data mimicked the original covariate structure. Different penalized versions of logistic regression as well as random forests and generalized additive models were investigated using classical logistic regression as a benchmark. Their performance was assessed based on measures of predictive accuracy, model discrimination, and model calibration. Three different scenarios using different subsets of the original data with different numbers of observations and events per variable were investigated. In the investigated setting, where a risk prediction model should be based on a small set of highly correlated and interconnected predictors, Elastic Net and also Ridge logistic regression showed good performance compared to their competitors, while other methods did not lead to substantial improvements or even performed worse than standard logistic regression. Our work demonstrates how simulation studies that mimic relevant features of a specific data set can support the choice of a good modeling strategy.     

Staining Sections of Peripheral Nerves for Axis Cylinders and for Myelin Sheaths

Pieces of mammalian nerves 1 to 2 cm. long were placed under moderate tension and fixed 24–48 hours in: picric acid, saturated aqueous, 90 ml.; formalin, 10 ml.; and trichloracetic acid, 25% aqueous, 2 ml. They were washed in water, cut in two and one end stained with 0.04–0.06% osmic acid solution, while the other was dehydrated, embedded in paraffin, and mounted sections from it stained with protargol. The fixing solution used was selected from a number of combinations of acidified picro-formalin as the one most likely to give satisfactory results when followed by both silver and osmic acid. The use of osmic acid solutions of less than 0.1% concentration avoided the overstaining of myelin sheaths seen frequently when stronger solutions were used with material that had been fixed previously. Protargol, 0.5% solution with fast green FCF added to make 0.05% dye in the final concentration, was used to impregnate sections for axis cylinders. Reduction and toning were done as in Bodian's method.     

Elastic network models capture the motions apparent within ensembles of RNA structures

The role of structure and dynamics in mechanisms for RNA becomes increasingly important. Computational approaches using simple dynamics models have been successful at predicting the motions of proteins and are often applied to ribonucleo-protein complexes but have not been thoroughly tested for well-packed nucleic acid structures. In order to characterize a true set of motions, we investigate the apparent motions from 16 ensembles of experimentally determined RNA structures. These indicate a relatively limited set of motions that are captured by a small set of principal components (PCs). These limited motions closely resemble the motions computed from low frequency normal modes from elastic network models (ENMs), either at atomic or coarse-grained resolution. Various ENM model types, parameters, and structure representations are tested here against the experimental RNA structural ensembles, exposing differences between models for proteins and for folded RNAs. Differences in performance are seen, depending on the structure alignment algorithm used to generate PCs, modulating the apparent utility of ENMs but not significantly impacting their ability to generate functional motions. The loss of dynamical information upon coarse-graining is somewhat larger for RNAs than for globular proteins, indicating, perhaps, the lower cooperativity of the less densely packed RNA. However, the RNA structures show less sensitivity to the elastic network model parameters than do proteins. These findings further demonstrate the utility of ENMs and the appropriateness of their application to well-packed RNA-only structures, justifying their use for studying the dynamics of ribonucleo-proteins, such as the ribosome and regulatory RNAs.