gebhart/patrepeval huggingface dataset:
Distinct interaction modes of an AKAP bound to two regulatory subunit isoforms of protein kinase A revealed by amide hydrogen/deuterium exchange (2005)

The structure of an AKAP docked to the dimerization/docking (D/D) domain of the type II (RIIalpha) isoform of protein kinase A (PKA) has been well characterized, but there currently is no detailed structural information of an AKAP docked to the type I (RIalpha) isoform. Dual-specific AKAP2 (D-AKAP2) binds in the nanomolar range to both isoforms and provided us with an opportunity to characterize the isoform-selective nature of AKAP binding using a common docked ligand. Hydrogen/deuterium (H/D) exchange combined with mass spectrometry (DXMS) was used to probe backbone structural changes of an alpha-helical A-kinase binding (AKB) motif from D-AKAP2 docked to both RIalpha and RIIalpha D/D domains. The region of protection upon complex formation and the magnitude of protection from H/D exchange were determined for both interacting partners in each complex. The backbone of the AKB ligand was more protected when bound to RIalpha compared to RIIalpha, suggesting an increased helical stabilization of the docked AKB ligand. This combined with a broader region of backbone protection induced by the AKAP on the docking surface of RIalpha indicated that there were more binding constraints for the AKB ligand when bound to RIalpha. This was in contrast to RIIalpha, which has a preformed, localized binding surface. These distinct modes of AKAP binding may contribute to the more discriminating nature of the RIalpha AKAP-docking surface. DXMS provides valuable structural information for understanding binding specificity in the absence of a high-resolution structure, and can readily be applied to other protein-ligand and protein-protein interactions.
In vivo regulation of plasminogen function by plasma carboxypeptidase B (2002)

The major functions of plasminogen (Plg) in fibrinolysis and cell migration depend on its binding to carboxy-terminal lysyl residues.The ability of plasma carboxypeptidase B (pCPB) to remove these residues suggests that it may act as a suppressor of these Plg functions.To evaluate this role of pCPB in vivo, homozygote pCPB-deficient mice were generated by homologous recombination, and the resulting pCPB -/-mice, which were viable and healthy, were mated to Plg -/-mice.Plg +/-mice show intermediate levels of fibrinolysis and cell migration compared with Plg wild-type and deficient mice, reflecting the intermediate levels of the Plg antigen in their plasma.Differences in Plg-dependent functions between pCPB +/+ , pCPB +/-, and pCPB -/-mice were then analyzed in a Plg +/-background.In a pulmonary clot lysis model, fibrinolysis was significantly increased in mice with partial (pCPB +/-) or total absence (pCPB -/-) of pCPB compared with their wild-type counterparts (pCPB +/+ ).In a thioglycollate model of peritoneal inflammation, leukocyte migration at 72 hours increased significantly in Plg +/-/pCPB +/-and Plg +/-/pCPB -/-compared with their wild-type counterparts.These studies demonstrate a definitive role of pCPB as a modulator of the pivotal functions of Plg in fibrinolysis and cell migration in vivo.
Dissemination of gonococcal infection is associated with delayed stimulation of complement-dependent neutrophil chemotaxis in vitro (1982)

Gonococci isolated from patients with uncomplicated gonorrhea or disseminated infection were examined for their ability to stimulate neutrophil chemotaxis in vitro. A neutrophil chemotactic response was not observed when as many as 10(9) colony-forming units of gonococci were incubated in buffer alone. However, a striking response was observed when 4 x 10(7) colony-forming units were incubated in 10% pooled normal human serum. Activation of complement was required for chemotaxis as demonstrated by complement consumption and failure of chemotactic activity generation in serum treated with heat or EDTA. Chromatography of activated serum demonstrated a single peak of chemotactic activity with an apparent molecular weight of 15,000 and was shown to be due to C5a. Examination of the kinetics of chemotactic factor generation demonstrated that local isolates stimulated a rapid response (about 60% maximal in 5 min), whereas the response to disseminated isolates was delayed (50% maximal in 20 to 30 min). Chemotactic activity generated by both types of isolates was suppressed at early time periods in agammaglobulinemic serum, indicating that immunoglobulins contribute to the generation of activity. Both pathways of complement activation were utilized by the two types of gonococci, but there was preferential dependence on the alternative pathway for disseminated strains and on the classical pathway for local isolates. We suggest that delayed stimulation of complement-dependent neutrophil migration may account in part for the infrequency of genital symptoms and may contribute to the mechanism of dissemination in patients with systemic gonococcal infection.
RBP1 Recruits the mSIN3-Histone Deacetylase Complex to the Pocket of Retinoblastoma Tumor Suppressor Family Proteins Found in Limited Discrete Regions of the Nucleus at Growth Arrest (2001)

Retinoblastoma (RB) tumor suppressor family pocket proteins induce cell cycle arrest by repressing transcription of E2F-regulated genes through both histone deacetylase (HDAC)-dependent and -independent mechanisms. In this study we have identified a stable complex that accounts for the recruitment of both repression activities to the pocket. One component of this complex is RBP1, a known pocket-binding protein that exhibits both HDAC-dependent and -independent repression functions. RB family proteins were shown to associate via the pocket with previously identified mSIN3-SAP30-HDAC complexes containing exclusively class I HDACs. Such enzymes do not interact directly with RB family proteins but rather utilize RBP1 to target the pocket. This mechanism was shown to account for the majority of RB-associated HDAC activity. We also show that in quiescent normal human cells this entire RBP1-mSIN3-SAP30-HDAC complex colocalizes with both RB family members and E2F4 in a limited number of discrete regions of the nucleus that in other studies have been shown to represent the initial origins of DNA replication following growth stimulation. These results suggest that RB family members, at least in part, drive exit from the cell cycle by recruitment of this HDAC complex via RBP1 to repress transcription from E2F-dependent promoters and possibly to alter chromatin structure at DNA origins.
A primary care approach to the patient with claudication. (2000)

Peripheral arterial occlusive disease occurs in about 18 percent of persons over 70 years of age. Usually, patients who have this disease present with intermittent claudication with pain in the calf, thigh or buttock that is elicited by exertion and relieved with a few minutes of rest. The disease may also present in a subacute or acute fashion. Symptoms of ischemic rest pain, ulceration or gangrene may be present at the most advanced stage of the disease. In most cases, the underlying etiology is atherosclerotic disease of the arteries. In caring for these patients, the primary care physician should focus on evaluation, risk factor modification and exercise. The physician should consider referral to a vascular subspecialist when symptoms progress or are severe. While the prognosis for the affected limb is quite good, patients with peripheral arterial occlusive disease are at increased risk of myocardial infarction and stroke. Therefore, treatment measures should address overall vascular health.
Formation of meizothrombin as intermediate in factor Xa-catalyzed prothrombin activation. (1986)

The conversion of prothrombin into thrombin by Factor Xa requires the cleavage of two peptide bonds in prothrombin. Dependent on the order of cleavage, prethrombin 2 or meizothrombin occurs as intermediate. Since prethrombin 2 has as yet been the only observed intermediate, prothrombin activation is generally considered to proceed via prethrombin 2. In this paper we present new methods that allow differentiation between meizothrombin and thrombin formed during the initial phase of prothrombin activation. These methods, which make use of the different reactivities of meizothrombin and thrombin toward fibrinogen and antithrombin III plus heparin, enabled us to show the generation of considerable amounts of meizothrombin during Factor Xa-catalyzed prothrombin activation. Both meizothrombin and thrombin incorporated the active site-directed fluorescent chloromethyl ketone 5-dimethylaminonaphthalene-1-sulfonyl-Glu-Gly-Arg-CH2Cl. Gel electrophoretic analysis of chloromethyl ketone-treated aliquots of prothrombin activation mixtures confirmed meizothrombin formation. These observations demonstrate that prothrombin may also be converted into thrombin via meizothrombin.
Components of a New Human Protein Kinase Signal Transduction Pathway (1995)

We have identified two components of a new protein kinase signaling cascade, MAPK/ERK kinase 5 (MEK5) and extracellular signal-regulated kinase 5 (ERK5). The MEK5 cDNA was isolated by degenerate PCR and encodes a 444-amino acid protein, which has approximately 40% identity to known MEKs. ERK5 was identified by a specific interaction with the MEK5 mutants S311A/T315A and K195M in the yeast two-hybrid system. The proteins were found to interact in an in vitro binding assay as well. ERK5 did not interact with MEK1 or MEK2. ERK5 is predicted to contain 815 amino acids and is approximately twice the size of all known ERKs. The C terminus of ERK5 has sequences which suggest that it may be targeted to the cytoskeleton. Sequences located in the N terminus of MEK5 may be important in coupling GTPase signaling molecules to the MEK5 protein kinase cascade. Both MEK5 and ERK5 are expressed in many adult tissue and are abundant in heart and skeletal muscle. A recombinant GST-ERK5 kinase domain displays autophosphorylation on Ser/Thr and Tyr residues.
Qualitative Improvement of Therapeutic Glycoproteins by Glycotechnology. (1992)

組織型プラスミノーゲン活性化因子、エリスロポイエチン、そして顆粒球-マクロファージ・コロニー刺激因子などの医療用蛋白質に関する最近の研究により、それらに付いている糖鎖は種々の生物的および物理的性質に重要な役割を果たしていることが明らかになった。顆粒球コロニー刺激因子とプロウロキナーゼに関する我々の研究の結果、N-結合型糖鎖を意図的に付加することにより、プロテアーゼ感受性、熱安定性、in vivo半減期の延長などのin vitroおよびin vivoの生物的諸性質を改善できることが示された。
Effects of Angiotensin-Converting Enzyme Inhibition on the Development of the Atrial Fibrillation Substrate in Dogs With Ventricular Tachypacing–Induced Congestive Heart Failure (2001)

CHF-induced increases in angiotensin II content and MAPK activation contribute to arrhythmogenic atrial structural remodeling. ACE inhibition interferes with signal transduction leading to the AF substrate in CHF and may represent a useful new component to AF therapy.
Transplantation of Cord-Blood Stem Cells into a Patient with Severe Thalassemia (1995)

Several different kinds of thalassemia and hemoglobinopathy are prevalent in Southeast Asia.1,2 The frequency of the α-thalassemias reaches 30 to 40 percent in northern Thailand, whereas the β-thalassemias occur at a frequency of 3 to 9 percent. Hemoglobin E, the hallmark hemoglobinopathy of Southeast Asia, occurs at a frequency of 50 to 60 percent at the junction of Thailand, Laos, and Cambodia. Mutation and gene interaction account for more than 60 different clinical syndromes. Of these, homozygous β-thalassemia and hemoglobin E –β-thalassemia disease are the most common and the most severe clinical syndromes compatible with live birth. Hemoglobin E–β-thalassemia . . .
Defects in Silicon Crystals Grown by the VLS Technique (1967)

Crystalline defects have been studied in silicon crystals grown by the vapor-liquid-solid (VLS) technique. Most of these crystals are highly perfect. However, some crystals contain defects such as dislocations, stacking faults, and second-phase regions. An elastic stress field, resulting from differential thermal contraction was found near the tip of every crystal. The formation and prevention of these defects and their relation to the VLS growth mechanism are discussed in detail. The morphology of the prismatic side faces of the crystals depends on deposition temperature, and is primarily due to vapor-solid deposit. This deposit is perfect even at deposition temperatures as low as 700°C.
Investigation of clay modifier effects on the structure and rheology of supercritical carbon dioxide‐processed polymer nanocomposites (2010)

Abstract Superior property enhancements in polymer–clay nanocomposites can be achieved if one can significantly enhance the nanoclay dispersion and polymer–clay interactions. Recent studies have shown that nanoclays can be dispersed in polymers using supercritical carbon dioxide (scCO 2 ). However, there is need for a better understanding of how changing the clay modifier affects the clay dispersability by scCO 2 and the resultant nanocomposite rheology. To address this, the polystyrene (PS)/clay nanocomposites with “weak” interaction (Cloisite 93A clay) and “strong” interaction (Cloisite 15A clay) have been prepared using the supercritical CO 2 method in the presence of a co‐solvent. Transmission electron microscopy images and small‐angle X‐ray diffraction illustrate that composites using 15A and 93A clays show similar magnitude of reduction in the average tactoid size, and dispersion upon processing with scCO 2 . When PS and the clays are coprocessed in scCO 2 , the “dispersion” of clays appears to be independent of modifier or polymer–clay interaction. However, the low‐frequency storage modulus in the scCO 2 ‐processed 15A nanocomposites is two orders of magnitude higher than that of 93A nanocomposites. It is postulated that below percolation (solution blended composites), the strength of polymer–clay interaction is not a significant contributor to rheological enhancement. In the scCO 2 ‐processed nanocomposites the enhanced dispersion passes the percolation threshold and the interactions dictate the reinforcement potential of the clay–polymer–clay network. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 823–831, 2010
Compartments of cyclic AMP and protein kinase in mammalian cardiomyocytes. (1983)

We have studied the compartmentation of cyclic AMP action in purified ventricular cardiomyocytes prepared by collagenase perfusion of adult rabbit hearts. Incubation of purified adult myocytes with 1 microM isoproterenol causes rapid accumulation of intracellular cyclic AMP in both soluble (2.3 leads to 7.7 pmol/ mg of protein) and particulate (3.0 leads to 9.2) fractions of cell homogenates (3000 X g for 5 min), increases in the total activity and activity ratio of soluble cyclic AMP-dependent protein kinase (0.21 leads to 0.66), a decrease in protein kinase activity remaining in the particulate fraction (47 leads to 30%), and an increase in the activity ratio of glycogen phosphorylase (0.15 leads to 0.47). Incubation of myocytes with 10 microM prostaglandin E1 (PGE1) leads to a comparable increase in soluble cyclic AMP (2.3 leads to 5.8 pmol/mg of protein) and activation of soluble cyclic AMP-dependent protein kinase (0.21 leads to 0.39) but does not result in any change in cAMP or protein kinase in the particulate fraction and fails to cause an activation of glycogen phosphorylase. PGE1 does not inhibit the effects of isoproterenol; when myocytes are incubated with both isoproterenol and PGE1, the accumulation of cyclic AMP, activation of cAMP-dependent protein kinase and phosphorylase b leads to a conversion are equal to that achieved with isoproterenol alone. Perturbation of cellular calcium using the ionophore A23187, verapamil, or high or low extracellular calcium did not alter the ability of isoproterenol to cause activation of particulate cAMP-dependent protein kinase or influence the inability of PGE1 to do so. Activation of adenylate cyclase by forskolin (30 microM) caused immediate activation of both soluble and particulate cAMP-dependent protein kinase leading to rapid activation of phosphorylase. We conclude that the hormonally specific compartmentation of cyclic AMP and cAMP-dependent protein kinase that occurs in intact heart (Hayes, J. S., Brunton, L. L., Brown, J. H., Reese, J. B., and Mayer, S. E. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 1570-1574) is not explained on the basis of cellular heterogeneity but has a subcellular basis within the cardiomyocyte.
Phosphatidylinositol 3-Kinase Encoded by Yeast VPS 34 Gene Essential for Protein Sorting (1993)

The VPS34 gene product (Vps34p) is required for protein sorting to the lysosome-like vacuole of the yeast Saccharomyces cerevisiae. Vps34p shares significant sequence similarity with the catalytic subunit of bovine phosphatidylinositol (PI) 3-kinase [the 110-kilodalton (p110) subunit of PI 3-kinase], which is known to interact with activated cell surface receptor tyrosine kinases. Yeast strains deleted for the VPS34 gene or carrying vps34 point mutations lacked detectable PI 3-kinase activity and exhibited severe defects in vacuolar protein sorting. Overexpression of Vps34p resulted in an increase in PI 3-kinase activity, and this activity was specifically precipitated with antisera to Vps34p. VPS34 encodes a yeast PI 3-kinase, and this enzyme appears to regulate intracellular protein trafficking decisions.
DNA‐Based Micelles: Synthesis, Micellar Properties and Size‐Dependent Cell Permeability (2010)

Functional nanomaterials based on molecular self-assembly hold great promise for applications in biomedicine and biotechnology. However, their efficacy could be a problem and can be improved by precisely controlling the size, structure, and functions. This would require a molecular engineering design capable of producing monodispersed functional materials characterized by beneficial changes in size, shape, and chemical structure. To address this challenge, we have designed and constructed a series of amphiphilic oligonucleotide molecules. In aqueous solutions, the amphiphilic oligonucleotide molecules, consisting of a hydrophilic oligonucleotide covalently linked to hydrophobic diacyllipid tails, spontaneously self-assemble into monodispersed, three-dimensional micellar nanostructures with a lipid core and a DNA corona. These hierarchical architectures are results of intermolecular hydrophobic interactions. Experimental testing further showed that these types of micelles have excellent thermal stability and their size can be fine-tuned by changing the length of the DNA sequence. Moreover, in the micelle system, the molecular recognition properties of DNA are intact, thus, our DNA micelles can hybridize with complimentary sequences while retaining their structural integrity. Importantly, when interacting with cell membranes, the highly charged DNA micelles are able to disintegrate themselves and insert into the cell membrane, completing the process of internalization by endocytosis. Interestingly, the fluorescence was found accumulated in confined regions of cytosole. Finally, we show that the kinetics of this internalization process is size-dependent. Therefore, cell permeability, combined with small sizes and natural nontoxicity are all excellent features that make our DNA-micelles highly suitable for a variety of applications in nanobiotechnology, cell biology, and drug delivery systems.
A new fermentation process allows large-scale production of human milk oligosaccharides by metabolically engineered bacteria (2002)

When fed to a beta-galactosidase-negative (lacZ(-)) Escherichia coli strain that was grown on an alternative carbon source (such as glycerol), lactose accumulated intracellularly on induction of the lactose permease. We showed that intracellular lactose was efficiently glycosylated when genes of glycosyltransferase that use lactose as acceptor were expressed. High-cell-density cultivation of lacZ(-) strains that overexpressed the beta 1,3 N acetyl glucosaminyltransferase lgtA gene of Neisseria meningitidis resulted in the synthesis of 6 g x L(-1) of the expected trisaccharide (GlcNAc beta 1-3Gal beta 1-4Glc). When the beta 1,4 galactosyltransferase lgtB gene of N. meningitidis was coexpressed with lgtA, the trisaccharide was further converted to lacto-N-neotetraose (Gal beta 1-4GlcNAc beta 1-3Gal beta 1-4Glc) and lacto-N-neoheaxose with a yield higher than 5 g x L(-1). In a similar way, the nanA(-) E. coli strain that was devoid of NeuAc aldolase activity accumulated NeuAc on induction of the NanT permease and the lacZ(-) nanA(-) strain that overexpressed the N. meningitidis genes of the alpha2,3 sialyltransferase and of the CMP-NeuAc synthase efficiently produced sialyllactose (NeuAc alpha 2-3Gal beta 1-4Glc) from exogenous NeuAc and lactose.
Anti-FGF23 Neutralizing Antibodies Show the Physiological Role and Structural Features of FGF23 (2008)

Fibroblast growth factor (FGF)23 is proposed to play a physiological role in the regulation of phosphate and vitamin D metabolism; deranged circulatory levels of FGF23 cause several diseases with abnormal mineral metabolism. This paper presents a novel approach to analyze the mechanism of action of FGF23 using anti-FGF23 monoclonal antibodies that can neutralize FGF23 activities both in vitro and in vivo. We developed two antibodies (FN1 and FC1) that recognize the N- and C-terminal regions of FGF23, respectively. Both FN1 and FC1 inhibited FGF23 activity in a cell-based Klotho-dependent reporter assay. Their administration caused marked increases in serum phosphate and 1,25D levels in normal mice. These changes were accompanied by altered expression in the kidney of type IIa sodium-phosphate cotransporter, 25-hydroxyvitamin-D-1alpha-hydroxylase, and 24-hydroxylase. Thus, this study using neutralizing antibodies confirms that FGF23 is a physiological regulator of phosphate and vitamin D metabolism. We addressed the mechanism of action for these neutralizing antibodies. Structural analysis of the FGF23/FN1-Fab complex showed that FN1 masked putative FGF receptor-binding sites in the N-terminal domain of FGF23, whereas biochemical analyses showed that FC1 interfered with the association between FGF23 and Klotho by binding to the C-terminal domain of FGF23. Taken together, our results suggest that the N- and C-terminal domains of FGF23 are responsible for association with cognate FGF receptors and Klotho, respectively, and that these interactions are indispensable for FGF23 activity.