Structure and stability of the insulin dimer investigated by molecular dynamics simulation

Molecular dynamics simulation indicates that the dynamical behaviour of the insulin dimer is asymmetric. Atomic level knowledge of the interaction modes and protein conformation in the solvation state identifies dynamical structures, held by hydrogen bonds that stabilize, mainly in one monomer, the interaction between the chains. Dynamic cross-correlation analysis shows that the two insulin monomers behave asymmetrically and are almost independent. Solvation energy, calculated to evaluate the contribute of each interface residue to the dimer association pattern, well compares with the experimental association state found in protein mutants indicating that this parameter is an important factor to explain the association properties of mutated insulin dimers.     

α-casein micelles-membranes interaction: Flower-like lipid protein coaggregates formation

BackgroundEnvironmental conditions regulate the association/aggregation states of proteins and their action in cellular compartments. Analysing protein behaviour in presence of lipid membranes is fundamental for the comprehension of many functional and dysfunctional processes. Here, we present an experimental study on the interaction between model membranes and α-casein. α-casein is the major component of milk proteins and it is recognised to play a key role in performing biological functions. The conformational properties of this protein and its capability to form supramolecular structures, like micelles or irreversible aggregates, are key effectors in functional and pathological effects.MethodsBy means of quantitative fluorescence imaging and complementary spectroscopic methods, we were able to characterise α-casein association state and the course of events induced by pH changes, which regulate the interaction of this molecule with membranes.ResultsThe study of these complex dynamic events revealed that the initial conformation of the protein critically regulates the fate of α-casein, size and structure of the newly formed aggregates and their effect on membrane structures. Disassembly of micelles due to modification in electrostatic interactions results in increased membrane structure rigidity which accompanies the formation of protein lipid flower-like co-aggregates with protein molecules localised in the external part.General significanceThese results may contribute to the comprehension of how the initial state of a protein establishes the course of events that occur upon changes in the molecular environment. These events which may occur in cells may be essential to functional, pathological or therapeutical properties specifically associated to casein proteins.     

Gene 5 protein of bacteriophage fd: A dimer which interacts Co-operatively with DNA

Isolated gene 5 protein from bacteriophage fd-infected Escherichia coli has been shown by sedimentation equilibrium to exist primarily as a dimer under non-denaturing conditions. The dimer was stable under conditions of high ionic strength, extremes in pH, dilution to 0.075 mg/ml, and increased temperature. Gene 5 protein did not undergo the indefinite self-association observed with gene 32 protein.Three lines of evidence for co-operative binding of gene 5 protein to DNA were developed. First, the interaction between gene 5 protein and phage T4 DNA was examined using a nitrocellulose filter assay. Scatchard plots of the binding data indicated that the interaction was co-operative. Similar results were obtained with gene 32 protein. Second, the co-operative binding of both proteins to DNA was shown by the sensitivity of the protein-DNA interaction to increasing ionic strength at various ratios of protein to DNA. Finally, by using the cross-linking agent, dimethyl suberixmidate, oligomeric structures containing at least seven monomers were found when the DNA was less than saturated.The possibility that gene 5 protein dimers undergo indefinite self-association in the presence of oligonucleotides was examined by sedimentation equilibrium. With oligo[d(pT)₄], the protein dimer was complexed with this oligonucleotide but no self-association was observed. With oligo[d(pT)₈], gene 5 protein formed tetramers, but no significant indefinite association was noted. These results do not suggest a DNA-induced conformational change, which results in indefinite association. A model for the co-operative binding of gene 5 protein to DNA is presented.     

Ultrafast dynamics-driven biomolecular recognition where fast activities dictate slow events

In general, biological macromolecules require significant dynamical freedom to carry out their different functions, including signal transduction, metabolism, catalysis and gene regulation. Effectors (ligands, DNA and external milieu, etc) are considered to function in a purely dynamical manner by selectively stabilizing a specific dynamical state, thereby regulating biological function. In particular, proteins in presence of these effectors can exist in several dynamical states with distinct binding or enzymatic activity. Here, we have reviewed the efficacy of ultrafast fluorescence spectroscopy to monitor the dynamical flexibility of various proteins in presence of different effectors leading to their biological activity. Recent studies demonstrate the potency of a combined approach involving picosecond-resolved Förster resonance energy transfer, polarisation-gated fluorescence and time-dependent stokes shift for the exploration of ultrafast dynamics in biomolecular recognition of various protein molecules. The allosteric protein–protein recognition following differential protein–DNA interaction is shown to be a consequence of some ultrafast segmental motions at the C-terminal of Gal repressor protein dimer with DNA operator sequences O_E and O_I. Differential ultrafast dynamics at the C-terminal of λ-repressor protein with two different operator DNA sequences for the protein–protein interaction with different strengths is also reviewed. We have also systemically briefed the study on the role of ultrafast dynamics of water molecules on the functionality of enzyme proteins α-chymotrypsin and deoxyribonuclease I. The studies on the essential ultrafast dynamics at the active site of the enzyme α-chymotrypsin by using an anthraniloyl fluorescent extrinsic probe covalently attached to the serine-195 residue for the enzymatic activity at homeothermic condition has also been reviewed. Finally, we have highlighted the evidence that a photoinduced dynamical event dictates the molecular recognition of a photochromic ligand, dihydroindolizine with the serine protease α-chymotrypsin and with a liposome (L-α-phosphatidylcholine).     

Association of insulin receptor and syndecan-1 by insulin with activation of ERK I/II in osteoblast-like UMR-106 cells

Abstract

Insulin plays an important role in various metabolic as well as anabolic actions in cells, including osteoblast cells. In the present study, we explored to determine if insulin receptor could associate with syndecan-1 in response to insulin and such association could lead to the activation of subsequent ERK I/II and alkaline phosphatase (ALP) in osteoblast cells. Insulin rapidly induces the association of insulin receptor with syndecan-1. Synstatin is a specific peptide inhibitor that blocks the binding of syndecan-1 to integrate. In the presence of synstatin, insulin-stimulated ERK I/II activation was dramatically inhibited, suggesting that syndecan-1/integrin interaction is essential in the activation of ERK I/II by insulin. Pretreatment of synstatin also inhibited the insulin-stimulated ALP activity. Taken together, these results suggest that insulin stimulates the association of insulin receptor with syndecan-1 and the complex formation of syndecan-1 and integrin could play an important role in ERK I/II–ALP signaling pathway in osteoblast cells.     

Quarternary Structure and Function in Phage λ Repressor: 1H-NMR Studies of Genetically Altered Proteins

Abstract

The quaternary structure and dynamics of phage λ repressor are investigated in solution by ¹H-NMR methods. λ repressor contains two domains separable by proteolysis: an N-terminal domain that mediates sequence-specific DNA-A binding, and a C-terminal domain that contains strong dimer and higher-order contacts. The active species in operator recognition is a dimer. Although the crystal structure of an N-terminal fragment has been determined, the intact protein has not been crystallized, and there is little evidence concerning its structure. ¹H-NMR data indicate that the N-terminal domain is only loosely tethered to the C-terminal domain, and that its tertiary structure is unperturbed by proteolysis of the “linker” polypeptide. It is further shown that in the intact repressor structure a quaternary interaction occurs between N-terminal domains. This domain-domain interaction is similar to the dimer contact observed in the crystal structure of the N-terminal fragment and involves the hydrophobic packing of symmetry-related helices (helix 5). In the intact structure this interaction is disrupted by the single amino-acid substitution, Ile84→Ser, which reduces operator affinity at least 100-fold. We conclude that quaternary interactions between N-terminal domains function to appropriately orient the DNA-binding surface with respect to successive major grooves of B-DNA.     

Regulation of the Protein Kinase Activity of the Human Insulin Receptor

Abstract

The insulin receptor is a hormone-dependent protein tyrosine kinase that belongs to the family of tyrosine kinases associated with growth factor receptors and oncogene products. The activity of the insulin receptor kinase is regulated by the phosphorylation state of specific domains of the protein. Phosphorylation of the receptor on tyrosine residues activates its kinase activity whereas phosphorylation on serine and/or threonine residues inhibits it. In this review, we discuss the evidence that supports a role of the kinase activity of the receptor in the molecular mechanism of insulin action.     

Socioeconomic position in childhood and adulthood and insulin resistance: cross sectional survey using data from British women's heart and health study

ObjectiveTo assess the associations between childhood and adulthood social class and insulin resistance.DesignCross sectional survey.Setting23 towns across England, Scotland, and Wales.Participants4286 women aged 60-79 years.ResultsBelonging to manual social classes in childhood and in adulthood was independently associated with increased insulin resistance, dyslipidaemia, and general obesity. The association between childhood social class and insulin resistance was stronger than that for adult social class. The effect, on insulin resistance and other risk factors, of belonging to a manual social class at either stage in the life course was cumulative, with no evidence of an interaction between childhood and adult social class. Women who were in manual social classes in childhood remained at increased risk of insulin resistance, dyslipidaemia, and obesity—even if they moved into non-manual social classes in adulthood—compared with women who were in non-manual social classes at both stages.ConclusionsAdverse social circumstances in childhood, as well as adulthood, are strongly and independently associated with increased risk of insulin resistance and other metabolic risk factors.

What is already known on this topic

Poor childhood social circumstances are, independently of adult social circumstances, associated with increased cardiovascular disease riskThey are associated with some components of the insulin resistance syndrome, and adverse childhood environmental factors, possibly poor nutrition, may lead to insulin resistance and to adult cardiovascular diseaseEvidence on the association between childhood social circumstances and insulin resistance in adulthood, and between childhood social circumstances and cardiovascular disease risk factors in women, is scarce

What this study adds

Belonging to manual social classes in childhood and in adulthood is independently associated with increased insulin resistance, dyslipidaemia, and obesity in older womenWomen who were in manual social classes in childhood remained at increased risk of insulin resistance, dyslipidaemia, and obesity, even if they had moved into non-manual social classes in adulthood     

Insulin activation of NADH ferricyanide reductase in human erythrocytes is mediated by the insulin receptor tyrosine kinase: a comparative study in normal and diabetic states

Summary

We have previously reported that NADH ferricyanide reductase in human erythrocytes is stimulated by insulin. Hormone-stimulated activities are attenuated in the presence of glycolytic inhibitors like vanadate, indicating the involvement of glycolysis in the mechanism by which insulin stimulates ferricyanide reduction. Activation of erythrocyte metabolism in response to insulin could be a result of hormone binding to its receptor, inducing phosphorylation of band 3 (at a site for reversible association of glycolytic enzymes) and/or other membrane proteins like the Na⁺/H⁺ antiport. Activation of the antiporter protein by insulin can stimulate glycolysis by an increase in intracellular pH, an effect which is prevented by amiloride. Evidence for a role for tyrosine phosphorylation in triggering the reductase activation came from studies with protein kinase inhibitors. Genistein, sphingosine and acridine orange have been shown to prevent insulin-stimulated ferricyanide reduction, implicating tyrosine phosphorylation as an important signal for activation of the enzyme by insulin. To evaluate activation of the enzyme by insulin stimulated phosphorylation, a comparative study was done using erythrocytes from healthy and diabetic humans. We measured ferricyanide reductase activities in basal and insulin stimulated states. Basal activities were lower in diabetics than in normal humans. Nevertheless, hormone stimulated activities were similar, despite earlier reports of decreased receptor phosphorylation of exogenous substrates in type 2 diabetics. These observations, together with previous ones, suggest that insulin-receptor kinase interaction may mediate the action of insulin on human erythrocytes by phosphorylation of cellular proteins like band 3 and/or the Na⁺/H⁺ antiport.     

Fluorescence studies on the coat protein of Alfalfa Mosaic Virus

Abstract

The intrinsic luminescence of different forms of the alfalfa mosaic virus (AMV) strain 425 coat protein has been studied, both statically and time resolved. It was found that the emission of the protein (M_r24,250), which contains two tryptophans at positions 54 and 190 and four tyrosines, is completely dominated by tryptophan fluorescence. The high fluorescence quantum yield indicates that both tryptophans are emitting. Surprisingly, the fluorescence decay is found to be strictly exponential, with a lifetime of 5.1 nsec. Similar results were obtained for various other forms of the protein, i.e. the 30-S polymer, the mildly trypsinised forms of the protein lacking the N-terminal part and the protein assembled into viral particles. Virus particles and proteins of stains S and VRU gave similar results, as well as the VRU protein polymerised into tubular structures. The fluorescence decay is also monoexponential in the presence of various concentrations of the quenching molecules acrylamide and potassium iodide. Stern-Volmer plots were linear and yield for the coat protein dimer with acrylamide a quenching constant of 4.5 ^* 10⁸ M^?1sec^?1. This indicates that the tryptophans are moderately accessible for acrylamide. For the 30-S polymer a somewhat smaller value was found, whereas in the viral Top a particles the accessibility of the tryptophans is still further reduced. From the decay of the polarisation anisotropy of the fluorescence of the coat protein dimer the rotational correlation time was obtained as 35 nsec. Since this roughly equals the expected rotational correlation time of the dimer as a whole, it suggests that the tryptophans are contained rigidly in the dimer.

The results show that in the excited state of the protein the two tryptophans are strongly coupled and suggest that the trp-trp distance is smaller than 10 A. Because the coat protein occurs as a dimer, the coupling can be inter- or intramolecular. The implications for the viral structure are discussed.     

Intermolecular Interaction of Fluoro Propanes

Abstract

Intermolecular interaction is investigated for an isomeric pair of fluoro propane, CH₃CF₂CF₃ (HFC–245cb, CB) and CH₂FCF₂CHF₂ (HFC–245ca, CA). CB has a larger dipole moment than CA. This may suggest that CB has a larger intermolecular attractive interaction than CA; the reverse is, however, found from the experimental data: normal boiling point, critical temperature, and heat of vaporization. Systematic ab initio calculations have been done for both CB dimer and CA dimer, and confirmed that the former has a smaller attractive interaction than the latter.

On the basis of these calculations, analytic functions have been constructed as the pair potential models for the two isomers. Each of these models has 11 Lennard-Jones and Coulomb interaction sites in the molecule. The present models can explain why CB dimer has a smaller attractive interaction than CA dimer, and they will easily be extended to a series of fluoro propanes, and make it possible to perform the systematic molecular simulation studies.     

Structural Investigations of Full-Length Insulin Receptor Dynamics and Signalling

Insulin regulates glucose homeostasis via binding and activation of the insulin receptor dimer at two distinct pairs of binding sites 1 and 2. Here, we present cryo-EM studies of full-length human insulin receptor (hIR) in an active state obtained at non-saturating, physiologically relevant insulin conditions. Insulin binds asymmetrically to the receptor under these conditions, occupying up to three of the four possible binding sites. Deletion analysis of the receptor together with site specific peptides and insulin analogs used in binding studies show that both sites 1 and 2 are required for high insulin affinity. We identify a homotypic interaction of the fibronectin type III domain (FnIII-3) of IR resulting in tight interaction of membrane proximal domains of the active, asymmetric receptor dimer. Our results show how insulin binding at two distinct types of sites disrupts the autoinhibited apo-IR dimer and stabilizes the active dimer. We propose an insulin binding and activation mechanism, which is sequential, exhibits negative cooperativity, and is based on asymmetry at physiological insulin concentrations with one to three insulin molecules activating IR.     

Structural and Thermodynamic Characterization of Vibrio fischeri CcdB

CcdB_Vfi from Vibrio fischeri is a member of the CcdB family of toxins that poison covalent gyrase-DNA complexes. In solution CcdB_Vfi is a dimer that unfolds to the corresponding monomeric components in a two-state fashion. In the unfolded state, the monomer retains a partial secondary structure. This observation correlates well with the crystal and NMR structures of the protein, which show a dimer with a hydrophobic core crossing the dimer interface. In contrast to its F plasmid homologue, CcdB_Vfi possesses a rigid dimer interface, and the apparent relative rotations of the two subunits are due to structural plasticity of the monomer. CcdB_Vfi shows a number of non-conservative substitutions compared with the F plasmid protein in both the CcdA and the gyrase binding sites. Although variation in the CcdA interaction site likely determines toxin-antitoxin specificity, substitutions in the gyrase-interacting region may have more profound functional implications.     

Crystal structure of cce_0566 from Cyanothece 51142, a protein associated with nitrogen fixation in the DUF269 family

The crystal structure for cce_0566 (171 aa, 19.4 kDa), a DUF269 annotated protein from the diazotrophic cyanobacterium Cyanothece sp. ATCC 51142, was determined to 1.60 Å resolution. Cce_0566 is a homodimer with each molecule composed of eight α-helices folded on one side of a three strand anti-parallel β-sheet. Hydrophobic interactions between the side chains of largely conserved residues on the surface of each β-sheet hold the dimer together. The fold observed for cce_0566 may be unique to proteins in the DUF269 family, hence, the protein may also have a function unique to nitrogen fixation. A solvent accessible cleft containing conserved charged residues near the dimer interface could represent the active site or ligand-binding surface for the protein’s biological function.Structured summary of protein interactionsDUF269 and DUF269 bind by x-ray crystallography (View interaction)     

The Spherical Expansion of H2 Dimer Interaction Energy by Double Symmetry-Adapted Perturbation Theory

Abstract

The weak interaction energy of H₂ dimer is studied by double symmetry-adapted perturbation theory (SAPT) within second-order of intermolecular and intramonomer perturbation for molecular simulations. The assumed orientations of H₂ dimer are linear, parallel, T type and X type. Among four orientations T orientation is the most stable, while linear orientation is the most repulsive. The second-order dispersion energy E _disp ⁽²⁾ is the most attractive contribution in all orientations. The interaction energy has the anisotropy, so we expressed our total interaction energy by the spherical expansion to compare with the experimental value. The isotropic interaction energy is about 85% of the experimental value.     

糖尿病前期和新诊断2型糖尿病患者血清血管内皮生长因子B水平与胰岛素抵抗的相关性

目的:探讨在糖尿病前期和新诊断2型糖尿病(T2DM)患者血清血管内皮生长因子B(VEGF-B)与胰岛素抵抗(IR)的关系。方法:选取2011年7月至2013年12月在我院内分泌科门诊就诊的患者419例,其中160例糖耐量正常(NGT)、142例糖尿病前期、117例新诊断T2DM患者,采用ELISA法测定血清VEGF-B水平,进一步分析血清VEGF-B水平与胰岛功能、胰岛素敏感性、肥胖及糖脂代谢相关代谢指标间的相关性。结果:血清VEGF-B水平在NGT (130.8 pg/mL [IQR 61.3-227.5])、糖尿病前期(146.7pg/mL [84.1-214.9])和T2DM(135.3 pg/mL [58.3-214.8])三组间无显著差异(P0.05)。相关分析显示血清VEGF-B水平与体重指数(BMI)、腰臀比(WHR)、血脂谱、胰岛功能及胰岛素敏感性均无相关性(P0.05)。结论:在糖尿病前期和新诊断T2DM患者,血清VEGF-B水平与肥胖、血脂谱、胰岛功能和胰岛素敏感性均无显著相关性,VEGF-B在人胰岛素抵抗及T2DM的发生中可能作用有限,仍需进一步研究明确其在代谢中的作用。     

Soft regions of protein surface are potent for stable dimer formation

Abstract

By having knowledge about the characteristics of protein interaction interfaces, we will be able to manipulate protein complexes for therapies. Dimer state is considered as the primary alphabet of the most proteins’ quaternary structure. The properties of binding interface between subunits and of noninterface region define the specificity and stability of the intended protein complex. Considering some topological properties and amino acids’ affinity for binding in interfaces of protein dimers, we construct the interface-specific recurrence plots. The data obtained from recurrence quantitative analysis, and accessibility-related metrics help us to classify the protein dimers into four distinct classes. Some mechanical properties of binding interfaces are computed for each predefined class of the dimers. The computed mechanical characteristics of binding patch region are compared with those of nonbinding region of proteins. Our observations indicate that the mechanical properties of protein binding sites have a decisive impact on determining the dimer stability. We introduce a new concept in analyzing protein structure by considering mechanical properties of protein structure. We conclude that the interface region between subunits of stable dimers is usually mechanically softer than the interface of unstable protein dimers. Abbreviations AAB average affinity for binding

ANM anisotropic network model

APC affinity propagation clustering

ASA accessible surface area

CCD inter residues distance

CSC complex stability code

DM distance matrix

ΔG_diss PISA-computed dissociation free energy

GNM Gaussian normal mode analysis

NMA normal mode analysis

PBP protein binding patch

PISA proteins, interfaces, structures and assemblies

rASA relative accessible area in respect to unfolded state of residues

RM recurrence matrix

rP relative protrusion

RP recurrence plot

RQA recurrence quantitative analysis

SEM standard error of mean

Communicated by Ramaswamy H. Sarma     

Birth weight of offspring and insulin resistance in late adulthood: cross sectional survey

ObjectiveTo investigate the association between birth weight of offspring and mothers'' insulin resistance in late adulthood.DesignCross sectional survey.SettingGeneral practitioner''s surgeries in 23 towns in Great Britain.Participants4286 women aged 60-79 years.ResultsBirth weight of offspring was inversely related to maternal insulin resistance in late adulthood. For each 1 kg higher birth weight of offspring, women had a 15% reduction in the odds of being in the fourth with highest insulin resistance, compared to other fourths (odds ratio 0.85; 95% confidence interval 0.71 to 1.00). This increased to 27% (0.73; 0.60 to 0.90) after adjusting data for potential confounders. A U shaped relation between birth weight of offspring and diabetes in older age was found; women with the lightest and heaviest offspring had the highest prevalence of diabetes.ConclusionsBirth weight of offspring is inversely related to the mother''s insulin resistance in late adulthood, despite the association of glucose intolerance during pregnancy with heavier offspring at birth. Common genetic factors contribute to the relation between birth weight and risk of cardiovascular disease and diabetes in adults.

What is already known on this topic

Small birth weight is related to increased risk of cardiovascular disease and diabetes in adulthood; the underlying mechanisms are unclearSmall birth weight of offspring is related to parental cardiovascular disease, suggesting that common genetic factors affect birth weight and the risk of disease in adulthoodGenetic factors associated with the metabolism of insulin are plausible in linking birth weight and cardiovascular disease (the fetal insulin hypothesis)

What this study adds

Birth weight of offspring is inversely related to maternal insulin resistance in older ageGenetic factors related to both insulin resistance and birth weight explain at least part of the association between birth weight and risk of cardiovascular disease and diabetes in adulthood