Collective Dynamics Underlying Allosteric Transitions in Hemoglobin

Hemoglobin is the prototypic allosteric protein. Still, its molecular allosteric mechanism is not fully understood. To elucidate the mechanism of cooperativity on an atomistic level, we developed a novel computational technique to analyse the coupling of tertiary and quaternary motions. From Molecular Dynamics simulations showing spontaneous quaternary transitions, we separated the transition trajectories into two orthogonal sets of motions: one consisting of intra-chain motions only (referred to as tertiary-only) and one consisting of global inter-chain motions only (referred to as quaternary-only). The two underlying subspaces are orthogonal by construction and their direct sum is the space of full motions. Using Functional Mode Analysis, we were able to identify a collective coordinate within the tertiary-only subspace that is correlated to the most dominant motion within the quaternary-only motions, hence providing direct insight into the allosteric coupling mechanism between tertiary and quaternary conformation changes. This coupling-motion is substantially different from tertiary structure changes between the crystallographic structures of the T- and R-state. We found that hemoglobin''s allosteric mechanism of communication between subunits is equally based on hydrogen bonds and steric interactions. In addition, we were able to affect the T-to-R transition rates by choosing different histidine protonation states, thereby providing a possible atomistic explanation for the Bohr effect.     

Sigmoidicity in Allosteric Models

We show results complementary to papers by Bardsley and Waight [2, 3], Gibson and Levin [13], Goldbeter [14], and Karlin [19] on sigmoidicity as an essential feature of allosteric models, possibly leading to a criterion of choice between these. In particular, we give the explicit form for the second derivative of the saturation function in the MWC case, and also the calculation of the binding polynomial in the circular KNF case. First, we give analytical conditions of sigmoidicity for each characteristic function in the MWC and KNF allosteric models. In the MWC model, the regions of sigmoidicity are different for the state and saturation functions, and when the catalytic activities of the two conformational states are different, the area of sigmoidicity is significantly larger for the steady-state rate function than for the saturation function. Furthermore, we rigorously prove the existence of mixed kinetic cooperativity in certain conditions. In the KNF model, the state and saturation functions are the same and their sigmoidicity depends only on the degree of coupling between subunits and on the relative stability of the asymmetrically induced subunit interactions. Finally, we suggest a theoretical criterion for discrimination between allosteric models.     

Allosteric interactions among drug binding sites on calmodulin

Felodipine is a fluorescent dihydropyridine Ca²⁺-antagonist. It binds to calmodulin in a Ca²⁺-dependent manner, and undergoes a fluorescence increase which allows us to monitor its interaction with calmodulin. Hydrophobic ligands including the calmodulin antagonist, R24571 and Ca²⁺ antagonists, prenylamine and diltiazem, bind to calmodulin and potentiate felodipine binding by as much as 20 fold. These studies suggest that allosteric interactions occur among different drug binding sites on calmodulin. Our results are discussed in terms of the mechanism of action of calmodulin.     

Propeller Twisting in Single Crystals of Nucleosides

Abstract

Propeller twists were measured for base-paired nucleosides and nucleic acid bases. The occurrence of propeller twist outside a double helical framework is shown, and conclusions drawn on the relative magnitude of the effect in single nucleosides.     

Hans Ussing, Experiments and Models

The article describes work and impact of Hans H. Ussing, a founder of epithelial physiology. Emphasis is on Ussing's model of epithelial transport, which showed early how a complex function can arise from a few basic principles. The KJU-model was developed 1958 for the amphibian epidermis and later applied and adapted to many epithelia, but especially to those that express amiloride-sensitive sodium channels in their apical membrane. Some of the subsequent research dealing with such channels and their cellular environment is briefly reviewed. The ideas of Hans Ussing were and are an inspiration to many of us, who continue to work in the way Ussing has taught us.     

On Semi-Parametric Models in Occult Tumour Experiments

Nonparametric statistical analyses of rodent carcinogenicity experiments involving occult tumours of intermediate lethality require numerous interim sacrifices. In recent papers, various semi-parametric analyses have been proposed which specify a parametric relationship between the death rate in tumour-bearing and tumour-free animals as a means of relaxing the requirement for multiple interim sacrifices. These semi-parametric methods involve different combinations of discrete and continuous time scales for the death and tumour-onset processes. The effect of combining different scales on this parametric relationship is studied further and illustrated via an example.     

The Database for Reaching Experiments and Models

Reaching is one of the central experimental paradigms in the field of motor control, and many computational models of reaching have been published. While most of these models try to explain subject data (such as movement kinematics, reaching performance, forces, etc.) from only a single experiment, distinct experiments often share experimental conditions and record similar kinematics. This suggests that reaching models could be applied to (and falsified by) multiple experiments. However, using multiple datasets is difficult because experimental data formats vary widely. Standardizing data formats promises to enable scientists to test model predictions against many experiments and to compare experimental results across labs. Here we report on the development of a new resource available to scientists: a database of reaching called the Database for Reaching Experiments And Models (DREAM). DREAM collects both experimental datasets and models and facilitates their comparison by standardizing formats. The DREAM project promises to be useful for experimentalists who want to understand how their data relates to models, for modelers who want to test their theories, and for educators who want to help students better understand reaching experiments, models, and data analysis.     

Influence of the Drying Technique of Silica Gels on the Enzymatic Activity of Encapsulated Lipase

Recent studies by Reetz et al. (Reetz, M.T., Zonta, A. and Simpelkamp, J. (1996a) Biotechnology and Bioengineering, 49, 527-534) have shown that the catalytic activity of lipase encapsulated in sol-gel materials, in esterification reactions, depends on many parameters such as the presence of hydrophobic groups grafted on the gel network and of an organic component in the gel network. In the present study, we have examined the effect of the gel pore texture which can be modified by varying the drying technique, for a given silica precursor composition and hydrolysis-condensation procedure. For a given mixture of two silane precursors, propyltri-methoxysilane and tetramethoxysilane, we compared the effects of the presence or absence of an organic component such as polyvinyl alcohol, in combination with drying either by evaporation which leads to the formation of xerogels, or by supercritical drying in CO₂ which leads to the formation of aerogels. For this last technique, the exchange of liquid is also an important step and its effect on the enzyme activity has been examined. The gel pore texture was characterized by nitrogen absorption according to the Brunauer Emmett and Teller method. The catalytic activities of the materials were compared in the esterification of lauric acid by 1-octanol.     

The Use of Carbon and Carmine Particles in Cell Fusion Experiments to Distinguish Hybrids from Parental Cells

The phagocytosis of inert particles, a long-known in vivo phenomenon among cells of the reticuloendothelial system, has more recently been found to be a widespread capability of cells in vitro (Gropp 1963) and can be utilized as a marking system when colored particles are employed. Carbon particles (black) were used by Stoker (1964) as cellular markers and later carmine particles (red) were used as markers in cell transformation studies (Stoker 1967; Rabinowitz and Sachs 1968).     

The Use of Carbon and Carmine Particles in Cell Fusion Experiments to Distinguish Hybrids from Parental Cells

The phagocytosis of inert particles, a long-known in vivo phenomenon among cells of the reticuloendothelial system, has more recently been found to be a widespread capability of cells in vitro (Gropp 1963) and can be utilized as a marking system when colored particles are employed. Carbon particles (black) were used by Stoker (1964) as cellular markers and later carmine particles (red) were used as markers in cell transformation studies (Stoker 1967; Rabinowitz and Sachs 1968).     

Voltage Clamp Experiments on Single Muscle Fibers of Rana pipiens

A voltage clamp for single muscle fibers has been developed. Stability of the system was achieved when an artificial node was created by enclosing a single muscle fiber in a petroleum jelly seal which served as an analogue of the myelin sheath. Typical voltage clamp records were obtained with large inward transient currents followed by a delayed rectification of the outward currents. These currents looked qualitatively similar when the transverse tubular system was destroyed. Errors in current measurement, especially those due to anomalous rectification, are discussed.     

Carboxylic and Dicarboxylic Acids Extracted from Crushed Magnesium Oxide Single Crystals

Carboxylic and dicarboxylic acids (glycolic, oxalic, malonic and succinic) have been extracted with tetrahydrofuran (THF) and H₂O from large synthetic MgO crystals, crushed to a medium fine powder. The extracts were characterized by infrared spectroscopy and ¹H-NMR. The THF extracts were derivatized with tert-butyldimethylsilyl (t-BDMS) for GC-MS analysis. A single crystal separated from the extract was used for an x-ray structure analysis, giving the monoclinic unit cell, space group P2₁/c with a_o = 5.543 Å, b_o = 8.845 Å, c_o = 5.086 Å, and = 91.9°, consistent with -succinic acid, HOOC(CH₂)COOH. The amount of extracted acids is estimated to be of the order of 0.1 to 0.5 mg g^-1 MgO. The MgO crystals from which these organic acids were extracted grew from the 2860 °C hot melt, saturated with CO/CO₂ and H₂O, thereby incorporating small amounts of the gaseous components to form a solid solution (ss) with MgO. Upon cooling, the ss becomes supersaturated, causing solute carbon and other solute species to segregate not only to the surface but also internally, to dislocations and subgrain boundaries. The organic acids extracted from the MgO crystals after crushing appear to derive from these segregated solutes that formed C–C, C–H and C–O bonds along dislocations and other defects in the MgO structure, leading to entities that can generically be described as (H_xC_yO_z)^n-. The processes underlying the formation of these precursors are fundamental in nature and expected to be operational in any minerals, preferentially those with dense structures, that crystallized in H₂O–CO₂-laden environments. This opens the possibility that common magmatic and metamorphic rocks when weathering at the surface of a tectonically active planet like Earth may be an important source of abiogenically formed complex organic compounds.     

A PCR Assay to Identify and Distinguish Single Juveniles of Meloidogyne hapla and M. chitwoodi

Random amplified polymorphic DNA (RAPD) bands that distinguish Meloidogyne hapla and M. chitwoodi from each other, and from other root-knot nematode species, were identified using a series of random octamer primers. The species-specific amplified DNA fragments were cloned and sequenced, and then the sequences were used to design 20-mer primer pairs that specifically amplified a DNA fragment from each species. Using the primer pairs, successful amplifications from single juveniles were readily attained. A mixture of four primers in a single PCR reaction mixture was shown to identify single juveniles of M. hapla and M. chitwoodi. To confirm specificity, the primers were used to amplify DNA from several isolates of M. hapla that originated from different crops and locations in North America and also from isolates of M. chitwoodi that differed in host range. In characterizing the M. hapla isolates, it was noted that there was a mitochondrial DNA polymorphism among isolates for cleavage by the restriction endonuclease DraI.     

Selective Allosteric Inhibition of MMP9 Is Efficacious in Preclinical Models of Ulcerative Colitis and Colorectal Cancer

Expression of matrix metalloproteinase 9 (MMP9) is elevated in a variety of inflammatory and oncology indications, including ulcerative colitis and colorectal cancer. MMP9 is a downstream effector and an upstream mediator of pathways involved in growth and inflammation, and has long been viewed as a promising therapeutic target. However, previous efforts to target matrix metalloproteinases (MMPs), including MMP9, have utilized broad-spectrum or semi-selective inhibitors. While some of these drugs showed signs of efficacy in patients, all MMP-targeted inhibitors have been hampered by dose-limiting toxicity or insufficient clinical benefit, likely due to their lack of specificity. Here, we show that selective inhibition of MMP9 did not induce musculoskeletal syndrome (a characteristic toxicity of pan-MMP inhibitors) in a rat model, but did reduce disease severity in a dextran sodium sulfate-induced mouse model of ulcerative colitis. We also found that MMP9 inhibition decreased tumor growth and metastases incidence in a surgical orthotopic xenograft model of colorectal carcinoma, and that inhibition of either tumor- or stroma-derived MMP9 was sufficient to reduce primary tumor growth. Collectively, these data suggest that selective MMP9 inhibition is a promising therapeutic strategy for treatment of inflammatory and oncology indications in which MMP9 is upregulated and is associated with disease pathology, such as ulcerative colitis and colorectal cancer. In addition, we report the development of a potent and highly selective allosteric MMP9 inhibitor, the humanized monoclonal antibody GS-5745, which can be used to evaluate the therapeutic potential of MMP9 inhibition in patients.     

An Orally Active Allosteric GLP-1 Receptor Agonist Is Neuroprotective in Cellular and Rodent Models of Stroke

Diabetes is a major risk factor for the development of stroke. Glucagon-like peptide-1 receptor (GLP-1R) agonists have been in clinical use for the treatment of diabetes and also been reported to be neuroprotective in ischemic stroke. The quinoxaline 6,7-dichloro-2-methylsulfonyl-3-N-tert- butylaminoquinoxaline (DMB) is an agonist and allosteric modulator of the GLP-1R with the potential to increase the affinity of GLP-1 for its receptor. The aim of this study was to evaluate the neuroprotective effects of DMB on transient focal cerebral ischemia. In cultured cortical neurons, DMB activated the GLP-1R, leading to increased intracellular cAMP levels with an EC₅₀ value about 100 fold that of exendin-4. Pretreatment of neurons with DMB protected against necrotic and apoptotic cell death was induced by oxygen-glucose deprivation (OGD). The neuroprotective effects of DMB were blocked by GLP-1R knockdown with shRNA but not by GLP-1R antagonism. In C57BL/6 mice, DMB was orally administered 30 min prior to middle cerebral artery occlusion (MCAO) surgery. DMB markedly reduced the cerebral infarct size and neurological deficits caused by MCAO and reperfusion. The neuroprotective effects were mediated by activation of the GLP-1R through the cAMP-PKA-CREB signaling pathway. DMB exhibited anti-apoptotic effects by modulating Bcl-2 family members. These results provide evidence that DMB, a small molecular GLP-1R agonist, attenuates transient focal cerebral ischemia injury and inhibits neuronal apoptosis induced by MCAO. Taken together, these data suggest that DMB is a potential neuroprotective agent against cerebral ischemia.     

固氮酶铬铁蛋白和锰铁蛋白大单晶的培养

用液 /液扩散法 ,从分别含Cr和Mn的无氨培养基中生长的固氮菌 (AzotobactervinelandiiLipmann)突变种UW3 中纯化出的CrFe蛋白和MnFe蛋白 ,在合适的结晶条件下生长出深棕色大单晶 (最大晶体的尺寸分别为 0 .2 0mm× 0 .2 0mm× 0 .0 7mm和 0 .18mm× 0 .18mm× 0 .0 5mm)。PEG、MgCl2 和NaCl的浓度对这两种蛋白的出晶时间、晶核数目、晶体大小和形状都有明显影响。结果表明 ,用此结晶法有利于CrFe蛋白和MnFe蛋白生长出可供X_射线衍射分析的大单晶。     

固氮酶铬铁蛋白和锰铁蛋白大单晶的培养

用液/液扩散法, 从分别含Cr和Mn的无氨培养基中生长的固氮菌(Azotobacter vinelandii Lipmann)突变种UW3中纯化出的CrFe蛋白和MnFe蛋白, 在合适的结晶条件下生长出深棕色大单晶(最大晶体的尺寸分别为0.20 mm×0.20 mm×0.07 mm 和 0.18 mm×0.18 mm×0.05 mm).PEG、MgCl2和NaCl 的浓度对这两种蛋白的出晶时间、晶核数目、晶体大小和形状都有明显影响.结果表明,用此结晶法有利于CrFe蛋白和MnFe蛋白生长出可供X-射线衍射分析的大单晶.