Regulation of mitochondrial contact sites in neonatal,juvenile and diabetic hearts

Mitochondrial contact sites (MiCS) are dynamic structures involved in high capacity transport of energy from mitochondria into the cytosole. Previous studies revealed that in normal conditions the actual number of MiCS is in correlation with the energy requirements of the heart, particularly with those for its contractile work. Although the detailed mechanisms of signalling between the processes of energy utilisation and MiCS formation in the heart are not yet elucidated, it is known that intracellular Ca²⁺ transients are intimately involved in this crosstalk. The present study is devoted to investigation of Ca²⁺-linked MiCS formation in healthy adult hearts and in hearts with modified Ca²⁺-handling such as in developing, in juvenile and diabetic myocardium. Experiments were performed on hearts of healthy rats on the 22nd embryonal day, 1st, 4th, 7th and 14th postnatal days as well as on adult hearts. Diabetic hearts were investigated on the 8th day after streptozotocin injection (45 mg.kg^–1 i.v.) to adult rats. Intracellular Ca²⁺ movements were affected by modulation of Ca²⁺ concentration in perfusion solution (1.6 or 2.2 mmol.l^–1) in isolated, Langendorff-perfused hearts, by calcium paradox (CaP) or by replacing of Ca²⁺ by Cd²⁺ ions. Elevation of extracellular Ca²⁺ was reflected by 30.1, 10.4 and 24.1% increase in intracellular free Ca²⁺ concentration in healthy adult, diabetic and 14-day old hearts respectively. In developing hearts the amount of MiCS was culminating on the 4th postnatal day. In adult hearts, elevated calcium in the perfusion solution, CaP as well as diabetes led to a significant increase in the amounts of MiCS formed (58.1, 77.2 and 86.5% respectively; p < 0.05). Diabetic and 14-day old hearts naturally exhibited amounts of MiCS comparable to those obtained by Ca²⁺-stimulation of MiCS formation in adult healthy hearts. In contrast to healthy controls, perfusion of diabetic and 14-day old hearts with elevated Ca²⁺ as well as induction of CaP exerted little influence on MiCS formation (4.4 and 8.2% for elevated Ca²⁺; 2.9 and 10.7% for CaP; p > 0.05). A replacement of Ca²⁺ by Cd²⁺ ions lowered the amount of MiCS in healthy adult and diabetic hearts (61 and 52.2%; p < 0.05). In conclusion, during development, the formation of MiCS may be influenced by both, permanent stimulation by Ca²⁺-signalling and the availability of mCPK. In healthy adult hearts the amount of MiCS is modulated by intracellular Ca²⁺ transients in response to changes in extracellular Ca²⁺ concentration. In diabetic hearts the modulation of MiCS formation is naturally attenuated, apparently as a consequence of persisting alterations in Ca²⁺-handling.     

Contact System. New Concepts on Activation Mechanisms and Bioregulatory Functions

This review considers the data of recent years concerning the contact system initiating the activation of blood plasma proteolytic systems, such as hemocoagulation, fibrinolysis, kininogenesis, and also complement and angiotensinogenesis. The main proteins of the contact system are the factors XII and XI, prekallikrein, and high-molecular-weight kininogen. The data on the structure, functions, and biosynthesis of these proteins and on their genes are presented. Studies in detail on the protein–protein interactions during formation of the ensemble of the contact system components on the anionic surface resulted in the postulation of the mechanism of activation of this system associated with generation of the XIIa factor and of kallikrein. This mechanism is traditionally considered a trigger of processes for the internal pathway of the hemocoagulating cascade. However, the absence of direct confirmation of such activation in vivo and the absence of hemorrhagia in the deficiency of these components stimulated the studies designed to find another mechanism of their activation and physiological role outside of the hemostasis system. As a result, a new concept on the contact system activation on the endothelial cell membrane was proposed. This concept is based on the isolation of a complex of proteins, which in addition to the above-mentioned proteins includes cytokeratin 1 and the receptors of the urokinase-like plasminogen activator and of the complement q-component. The ideas on the role of this system in the biology of vessels are developed. Some of our findings on the effect of leukocytic elastase on the key components of the contact system are also presented.     

Simplicial edge representation of protein structures and alpha contact potential with confidence measure

Protein representation and potential function are two important ingredients for studying protein folding, equilibrium thermodynamics, and sequence design. We introduce a novel geometric representation of protein contact interactions using the edge simplices from the alpha shape of the protein structure. This representation can eliminate implausible neighbors that are not in physical contact, and can avoid spurious contact between two residues when a third residue is between them. We developed statistical alpha contact potential using an odds-ratio model. A studentized bootstrap method was then introduced to assess the 95% confidence intervals for each of the 210 propensity parameters. We found, with confidence, that there is significant long-range propensity (>30 residues apart) for hydrophobic interactions. We tested alpha contact potential for native structure discrimination using several sets of decoy structures, and found that it often performs comparably with atom-based potentials requiring many more parameters. We also show that accurate geometric representation is important, and that alpha contact potential has better performance than potential defined by cutoff distance between geometric centers of side chains. Hierarchical clustering of alpha contact potentials reveals natural grouping of residues. To explore the relationship between shape and physicochemical representations, we tested the minimum alphabet size necessary for native structure discrimination. We found that there is no significant difference in performance of discrimination when alphabet size varies from 7 to 20, if geometry is represented accurately by alpha simplicial edges. This result suggests that the geometry of packing plays an important role, but the specific residue types are often interchangeable.     

An improved model of association for VH-VL immunoglobulin domains: asymmetries between VH and VL in the packing of some interface residues

The antibody-binding site is formed as a result of the association between VH and VL domains. Several studies have shown that this association plays an important role in the mechanism of antigen-antibody interaction (Stanfield et al. Structure 1: 83-93, 1993). Considering this, we propose that variations in the VH-VL association are part of the diversification strategy of the antibody repertoires. Previously, a model of association for VH-VL domains based on geometrical characteristics of the packing at the interface was developed by Chothia et al. (J. Mol. Biol. 186: 61-663, 1985). This model includes a common association form for antibodies and a three-layer structure for the interface. In the present work, a complementary model is introduced to account for the general geometrical restrictions of the VH-VL interface, and particular arrangements related to the chemical properties or the side-chain orientations of participating residues. Groups of residues assume common side-chain orientations, which are apparently related to particular functions of different interface zones. Analyses of amino acid usage and network are in agreement with the side-chain orientation patterns. Based on these observations, a three-zone model has evolved to illuminate geometrical and functional restrictions acting over the VH-VL interface. Additionally, this study has revealed the asymmetrical relationships between VH and VL residues important for the association of the two domains.     

The zyxin-related protein TRIP6 interacts with PDZ motifs in the adaptor protein RIL and the protein tyrosine phosphatase PTP-BL

The small adaptor protein RIL consists of two segments, the C-terminal LIM and the N-terminal PDZ domain, which mediate multiple protein-protein interactions. The RIL LIM domain can interact with PDZ domains in the protein tyrosine phosphatase PTP-BL and with the PDZ domain of RIL itself. Here, we describe and characterise the interaction of the RIL PDZ domain with the zyxin-related protein TRIP6, a protein containing three C-terminal LIM domains. The second LIM domain in TRIP6 is sufficient for a strong interaction with RIL. A weaker interaction with the third LIM domain in TRIP6, including the proper C-terminus, is also evident. TRIP6 also interacts with the second out of five PDZ motifs in PTP-BL. For this interaction to occur both the third LIM domain and the proper C-terminus are necessary. RNA expression analysis revealed overlapping patterns of expression for TRIP6, RIL and PTP-BL, most notably in tissues of epithelial origin. Furthermore, in transfected epithelial cells TRIP6 can be co-precipitated with RIL and PTP-BL PDZ polypeptides, and a co-localisation of TRIP6 and RIL with Factin structures is evident. Taken together, PTP-BL, RIL and TRIP6 may function as components of multi-protein complexes at actin-based sub-cellular structures.     

Large-sliding contact elements accurately predict levels of bone-implant micromotion relevant to osseointegration

Primary stability is recognised as an important determinant in the aseptic loosening failure process of cementless implants. An accurate evaluation of the bone–implant relative micromotion is becoming important both in pre-clinical and clinical studies. If the biological threshold for micro-movements is in the range 100–200 μm then, in order to be discriminative, any method used to evaluate the primary stability should have an accuracy of 10–20 μm or better. Additionally, such method should also be able to report the relative micromotion at each point of the interface. None of the available experimental methods satisfies both requirements. Aim of the present study is to verify if any of the current finite element modelling techniques is sufficiently accurate in predicting the primary stability of a cementless prosthesis to be used to decide whether the micromotion may or may not jeopardise the implant osseointegration. The primary stability of an anatomic cementless stem, as measured in vitro, was used as a benchmark problem to comparatively evaluate different contact modelling techniques. Frictionless contact, frictional contact and press-fitted frictional contact conditions were modelled using alternatively node-to-node, node-to-face and face-to-face contact elements. The model based on face-to-face contact elements accounting for frictional contact and initial press-fit was able to predict the micromotion measured experimentally with an average (RMS) error of 10 μm and a peak error of 14 μm. All the other models presented errors higher than 20 μm assumed in the present study as an accuracy threshold.     

How do potentials derived from structural databases relate to “true” potentials?

Knowledge-based potentials are used widely in protein folding and inverse folding algorithms. Two kinds of derivation methods are used. (1) The interactions in a database of known protein structures are assumed to obey a Boltzmann distribution. (2) The stability of the native folds relative to a manifold of misfolded structures is optimized. Here, a set of previously derived contact and secondary structure propensity potentials, taken as the "true" potentials, are employed to construct an artificial protein structural database from protein fragments. Then, new sets of potentials are derived to see how they are related to the true potentials. Using the Boltzmann distribution method, when the stability of the structures in the database lies within a certain range, both contact potentials and secondary structure propensities can be derived separately with remarkable accuracy. In general, the optimization method was found to be less accurate due to errors in the "excess energy" contribution. When the excess energy terms are kept as a constraint, the true potentials are recovered exactly.     

A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR,X‐ray,and computations

A detailed analysis of high‐resolution structural data and computationally predicted dynamics was carried out for a designed sugar‐binding protein. The mean‐square deviations in the positions of residues derived from nuclear magnetic resonance (NMR) models and those inferred from X‐ray crystallographic B‐factors for two different crystal forms were compared with the predictions based on the Gaussian Network Model (GNM) and the results from molecular dynamics (MD) simulations. GNM systematically yielded a higher correlation than MD, with experimental data, suggesting that the lack of atomistic details in the coarse‐grained GNM is more than compensated for by the mathematically exact evaluation of fluctuations using the native contacts topology. Evidence is provided that particular loop motions are curtailed by intermolecular contacts in the crystal environment causing a discrepancy between theory and experiments. Interestingly, the information conveyed by X‐ray crystallography becomes more consistent with NMR models and computational predictions when ensembles of X‐ray models are considered. Less precise (broadly distributed) ensembles indeed appear to describe the accessible conformational space under native state conditions better than B‐factors. Our results highlight the importance of using multiple conformations obtained by alternative experimental methods, and analyzing results from both coarse‐grained models and atomic simulations, for accurate assessment of motions accessible to proteins under native state conditions. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

织物电极的皮肤-电极接触阻抗测量方法分析

随着可穿戴式健康监测技术的发展,新型心电传感器-织物电极成为人们关注的热点,本文对织物电极的皮肤-电极接触阻抗测量方法进行了综述。首先介绍了织物电极的概念,分析了织物电极的皮肤-电极电化学界面、皮肤-电极电化学界面的等效电路和简化电路模型,得出了皮肤-电极接触阻抗的计算公式;其次,将皮肤-电极接触阻抗的测量方法归纳为直接测量法、参比测量法和模拟皮肤测量法三类,讨论了它们的测量原理和优缺点。本文认为需将模拟皮肤测量法和真实皮肤测量法有机结合,才能有效评价织物电极的阻抗特性,为织物电极的性能评价和心电信号采集电路的设计提供重要依据。最后,本文对织物电极待解决的问题进行了分析讨论。