A milestoning study of the kinetics of an allosteric transition: atomically detailed simulations of deoxy Scapharca hemoglobin

Atomically detailed simulations are used to compute the kinetics of the R-to-T transition in deoxy Scapharca hemoglobin. A computational approach called milestoning is utilized that combines 1), an efficient reaction path algorithm; and 2), a "fragment and glue" approach for classical trajectories. Milestoning computes the R-to-T transition kinetics on the microsecond timescale based on atomically detailed trajectories that rarely exceed a nanosecond. Eleven reference hypersurfaces (milestones) are constructed along the reaction coordinate, which is computed with a global path optimization algorithm. Two-hundred classical trajectories are calculated for each of the milestones to collect local distributions of first passage times. These local distributions are used in a non-Markovian theory to compute the overall timescale. Exponential enrichment of reactive trajectories, an important component of the milestoning approach, makes these calculations possible. The overall timescale of the reaction is estimated as 10 +/- 9 micros, in accord with available experimental data. The barrier is not sharp and is spread over four milestones. Even after the most significant structural changes are completed (phenylalanine F4 ring flips), highly collective and activated motions continue. The calculations suggest an additional late free energy barrier.     

Coordinated movement of RACK1 with activated betaIIPKC.

Protein kinase C (PKC) isozymes move upon activation from one intracellular site to another. PKC-binding proteins, such as receptors for activated C kinase (RACKs), play an important role in regulating the localization and diverse functions of PKC isozymes. RACK1, the receptor for activated betaIIPKC, determines the localization and functional activity of betaIIPKC. However, the mechanism by which RACK1 localizes activated betaIIPKC is not known. Here, we provide evidence that the intracellular localization of RACK1 changes in response to PKC activation. In Chinese hamster ovary cells transfected with the dopamine D2L receptor and in NG108-15 cells, PKC activation by either phorbol ester or a dopamine D2 receptor agonist caused the movement of RACK1. Moreover, PKC activation resulted in the in situ association and movement of RACK1 and betaIIPKC to the same intracellular sites. Time course studies indicate that PKC activation induces the association of the two proteins prior to their co-movement. We further show that association of RACK1 and betaIIPKC is required for the movement of both proteins. Our results suggest that RACK1 is a PKC shuttling protein that moves betaIIPKC from one intracellular site to another.     

A Shared Endoplasmic Reticulum-associated Degradation Pathway Involving the EDEM1 Protein for Glycosylated and Nonglycosylated Proteins

Studies of misfolded protein targeting to endoplasmic reticulum-associated degradation (ERAD) have largely focused on glycoproteins, which include the bulk of the secretory proteins. Mechanisms of targeting of nonglycosylated proteins are less clear. Here, we studied three nonglycosylated proteins and analyzed their use of known glycoprotein quality control and ERAD components. Similar to an established glycosylated ERAD substrate, the uncleaved precursor of asialoglycoprotein receptor H2a, its nonglycosylated mutant, makes use of calnexin, EDEM1, and HRD1, but only glycosylated H2a is a substrate for the cytosolic SCF^Fbs2 E3 ubiquitin ligase with lectin activity. Two nonglycosylated BiP substrates, NS-1κ light chain and truncated Igγ heavy chain, interact with the ERAD complex lectins OS-9 and XTP3-B and require EDEM1 for degradation. EDEM1 associates through a region outside of its mannosidase-like domain with the nonglycosylated proteins. Similar to glycosylated substrates, proteasomal inhibition induced accumulation of the nonglycosylated proteins and ERAD machinery in the endoplasmic reticulum-derived quality control compartment. Our results suggest a shared ERAD pathway for glycosylated and nonglycosylated proteins composed of luminal lectin machinery components also capable of protein-protein interactions.     

Urochordate betagamma-crystallin and the evolutionary origin of the vertebrate eye lens

A refracting lens is a key component of our image-forming camera eye; however, its evolutionary origin is unknown because precursor structures appear absent in nonvertebrates. The vertebrate betagamma-crystallin genes encode abundant structural proteins critical for the function of the lens. We show that the urochordate Ciona intestinalis, which split from the vertebrate lineage before the evolution of the lens, has a single gene coding for a single domain monomeric betagamma-crystallin. The crystal structure of Ciona betagamma-crystallin is very similar to that of a vertebrate betagamma-crystallin domain, except for paired, occupied calcium binding sites. The Ciona betagamma-crystallin is only expressed in the palps and in the otolith, the pigmented sister cell of the light-sensing ocellus. The Ciona betagamma-crystallin promoter region targeted expression to the visual system, including lens, in transgenic Xenopus tadpoles. We conclude that the vertebrate betagamma-crystallins evolved from a single domain protein already expressed in the neuroectoderm of the prevertebrate ancestor. The conservation of the regulatory hierarchy controlling betagamma-crystallin expression between organisms with and without a lens shows that the evolutionary origin of the lens was based on co-option of pre-existing regulatory circuits controlling the expression of a key structural gene in a primitive light-sensing system.     

A deleterious effect associated with UNH159 is attenuated in twin embryos of an inbred line of blue tilapia Oreochromis aureus

Offspring of a highly inbred gynogenetic line of Oreochromis aureus displayed 12‐fold increase in twinning rate compared to the outbred population. Asymmetric conjoined twins, which consist of a normal embryo attached to a malformed‐atrophic twin, were frequently encountered in both gynogenetic (90·7%) and outbred (38·2%) embryos. The monozygotic origin of these twins was determined using five microsatellite markers. Progeny of heterozygous parents for the microsatellite UNH159 were separated into sub‐sets of twins and normal full‐sibs. Consistent with previous reports, the normal embryo sub‐set exhibited elimination of both types of homozygotes for the UNH159 genetic marker at 2–8 days after fertilization. Unexpectedly, this elimination was less frequent in twins. The UNH159 marker as well as RNA‐binding motif protein, X‐linked (rbmx), SRY‐box containing gene 3 (sox3) and alpha‐thalassemia/mental retardation syndrome X‐linked (atrx) genes were mapped to linkage group 2. These gene orthologues are all located on the mammalian X chromosome and atrx is necessary for the X‐chromosome inactivation.     

Glial cell line-derived neurotrophic factor reverses ethanol-mediated increases in tyrosine hydroxylase immunoreactivity via altering the activity of heat shock protein 90

We previously found that glial cell line-derived neurotrophic factor (GDNF) in the midbrain ventral tegmental area (VTA) negatively regulates alcohol drinking (He, D. Y., McGough, N. N., Ravindranathan, A., Jeanblanc, J., Logrip, M. L., Phamluong, K., Janak, P. H., and Ron, D. (2005) J. Neurosci. 25, 619-628). Several studies suggest a role for GDNF in the regulation of tyrosine hydroxylase (TH) levels in the midbrain (Georgievska, B., Kirik, D., and Bjorklund, A. (2004) J. Neurosci. 24, 6437-6445). Up-regulation of TH levels has been reported as a hallmark of biochemical adaptations to in vivo chronic exposure to drugs of abuse, including ethanol (Ortiz, J., Fitzgerald, L. W., Charlton, M., Lane, S., Trevisan, L., Guitart, X., Shoemaker, W., Duman, R. S., and Nestler, E. J. (1995) Synapse 21, 289-298). We hypothesized that GDNF plays an important role in regulating prolonged ethanol-mediated increases in TH protein levels. Using the SH-SY5Y dopaminergic-like cell line, we found that the increase in TH levels in the presence of ethanol required the activation of the cAMP/PKA pathway and was reversed by GDNF. Ethanol treatment did not alter the mRNA level or protein translation of TH, but enhanced the stability of the protein that was decreased by GDNF. Interestingly, we observed that ethanol treatment resulted in an increase in TH association with the chaperone heat shock protein (HSP90) that was mediated by the cAMP/PKA pathway and inhibited by GDNF. Taken together, these data suggest that prolonged ethanol exposure leads to increased association of TH and HSP90 via the cAMP/PKA pathway, resulting in the stabilization and subsequent accumulation of TH. GDNF reverses this ethanol-mediated adaptation by inhibiting the interaction of TH with HSP90.     

Initiation of deoxyribonucleic acid replication in Escherichia coli B: uncoupling from mass/deoxyribonucleic acid ratio.

In Escherichia coli growing at different rates, the ratio of cell mass to the number of chromosome origins tended to be constant at the time of the initiation of deoxyribonucleic acid (DNA) replication. This observation led to the assumption that the initiation event is controlled in some way by cell mass, e.g., by a growth-dependent synthesis of an initiator or dilution of a repressor. We have now found that the initiation of DNA synthesis can be uncoupled from cell mass. We used a synchronous culture of newly divided cells of E. coli B which was obtained by the membrane elution technique (C.E. Helmstetter, J. Mol. Biol. 24: 417-427, 1967) and was starved for an amino acid. Upon restoration of the amino acid, the cells not only divided at a size that was smaller than normal, but also initiated DNA replication long before they could increase their masses to reach the expected ratio of mass/DNA presumably required for initiation.     

Stability of helix-rich proteins at high concentrations

A number of techniques, including circular dichroism, FTIR, front face fluorescence, and UV absorption spectrophotometries, dynamic light scattering, and DSC, were used to directly measure the colloidal and conformational stability of proteins in highly concentrated solutions. Using bovine serum albumin (BSA), chicken egg white lysozyme, human hemoglobin A0, and bovine fibrinogen as model proteins, the thermal transition temperatures of proteins in dilute and concentrated solutions were compared. At 10 degrees C, no significant differences in both secondary and tertiary structures were detected for proteins at different concentrations. When temperature was introduced as a variable, however, hemoglobin and fibrinogen demonstrated higher transition midpoints (T(m)s) in concentrated rather than in dilute solutions (deltaT(m) approximately 2-10 degrees C). In contrast, lysozyme and BSA in concentrated solutions exhibit a lower T(m) than in dilute solutions (deltaT(m) approximately 2-20 degrees C). From these studies, it appears that a variety of factors determine the effect of high concentrations on the colloidal and conformational stability of a particular protein. While the prediction of excluded volume theory is that high concentrations should conformationally stabilize proteins, other factors such as pH, kinetics, protein dynamics, and intermolecular charge-charge effects may affect the overall stability of proteins at high concentrations under certain conditions.     

Snail基因及其蛋白、E-cadherin蛋白在胃癌中的表达及其临床意义

目的观察Snail mRNA及其蛋白、E-cadherin蛋白在胃癌组织中的表达及其与胃癌临床病理特征的关系,并探讨它们在胃癌发生、发展中的作用及其临床应用价值。方法收集96例手术切除胃癌标本,同时取80例癌旁组织作为对照。应用免疫组织化学S-P法检测胃癌组织、癌旁组织中snail蛋白、E-cadherin蛋白的表达;运用原位分子杂交技术检测胃癌组织、癌旁组织中Snail mRNA的表达。结果（1）Snail蛋白在胃癌组织阳性率（83.3%）显著高于癌旁组织（41.25%）（P〈0.05）;高、中分化组Snail蛋白阳性表达率显著低于低分化组（P〈0.05）;Snail蛋白的阳性表达率在乳头状腺癌、管状腺癌及低分化腺癌与黏液癌之间差异有显著性（P〈0.05）;Snail蛋白的表达与胃癌浸润深度、淋巴结转移及远处转移有关（P〈0.05）,与性别、年龄、肿瘤大小、肿瘤部位及临床分期无关（P〉0.05）;（2）胃癌组织中snail mR-NA的阳性率（76%）显著高于癌旁组织（30%）（P〈0.05）;高、中分化组Snail mRNA阳性表达率显著低于低分化组（P〈0.05）;Snail mRNA的阳性表达率在乳头状腺癌、管状腺癌及低分化腺癌与黏液癌之间差异有显著性（P〈0.05）;Snail mRNA的表达与浸润深度及淋巴结转移有关（P〈0.05）,与性别、年龄、肿瘤大小、肿瘤部位、临床分期及远处转移无关（P〉0.05）;（3）E-cadherin蛋白在胃癌组织阳性率（37.5%）显著低于癌旁组织（100%）（P〈0.05）;高、中分化组E-cadherin蛋白阳性率显著高于低分化组（P〈0.05）;E-cadherin蛋白阳性率在乳头状腺癌、管状腺癌及低分化腺癌与黏液癌之间差异有显著性（P〈0.05）;E-cadherin蛋白的表达与胃癌浸润深度、淋巴结转移、临床分期及远处转移有关（P〈0.05）,与性别、年龄、肿瘤大小、肿瘤部位均无关（P〉0.05）;（4）胃癌组织中snail mRNA和snail蛋白的表达呈正相关（r=0.594,P〈0.05）;Snail蛋白和E-cadherin蛋白的表达呈负相关（r=-0.234,P〈0.05）。结论（1）E-cadher-in蛋白低表达与Snail蛋白高表达可能是胃黏膜恶性转变以及胃癌发生浸润转移的重要生物学标志;联合检测E-cadherin蛋白与Snail蛋白对预测胃癌浸润转移有重要意义。（2）Snail蛋白可能在转录水平上调控E-cadherin蛋白的表达。