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Riddhi Shah, Andrew T Large, Astrid Ursinus, Bevan Lin, Preethy Gowrinathan, Jörg Martin, Peter A Lund
UNLABELLED: Chaperonins are required for correct folding of many proteins. They exist in two phylogenetic groups: group I, found in bacteria and eukaryotic organelles, and group II, found in archaea and eukaryotic cytoplasm. The two groups, while homologous, differ significantly in structure and mechanism. The evolution of group II chaperonins has been proposed to have been crucial in enabling the expansion of the proteome required for eukaryotic evolution. In an archaeal species that expresses both groups of chaperonins, client selection is determined by structural and biochemical properties rather than phylogenetic origin...
October 1, 2016: Journal of Bacteriology
Ryan S Ritterson, Daniel Hoersch, Kyle A Barlow, Tanja Kortemme
In recent years, interest in controlling protein function with light has increased. Light offers a number of unique advantages over other methods, including spatial and temporal control and high selectivity. Here, we describe a general protocol for engineering a protein to be controllable with light via reaction with an exogenously introduced photoisomerizable small molecule and illustrate our protocol with two examples from the literature: the engineering of the calcium affinity of the cell-cell adhesion protein cadherin, which is an example of a protein that switches from a native to a disrupted state (Ritterson et al...
2016: Methods in Molecular Biology
Michael Vouche, Riad Salem, Robert J Lewandowski, Frank H Miller
AIM: To compare changes in RECIST, anatomical volume, mRECIST, and volumetric diffusion-weighted Imaging parameters (3D apparent diffusion coefficient (ADC) measurements), with pathological analysis of hepatocellular carcinoma (HCC) treated by (90)Yttrium radioembolization (Y90). METHODS: 21 patients were treated by Y90 as a sole treatment modality for solitary, >2 cm HCC that underwent liver transplantation. MRI at baseline, 1 and 3 months post-Y90, and tumor pathological findings on explants were reviewed in all patients...
August 2015: Abdominal Imaging
Gregory Hildebrand, Marc Tompkins, Jeffrey Macalena
PURPOSE: The purpose of this study was to identify the relationship between the common peroneal nerve (CPN) and the fibular head. METHODS: Sixteen cadaveric dissections were performed. The distance from the fibular head to the center of the CPN as it exits beneath the biceps femoris (BF) was measured in 0°, 30°, 60°, and 90° of flexion and was averaged on the first 8 specimens. Based on those measurements, a needle was placed on the second 8 dissections before the fascial incision was made to assess reliability...
January 2015: Arthroscopy: the Journal of Arthroscopic & related Surgery
Hoomin Lee, SangJae Seo, Minhyeok Kim, Jae boong Choi, Sun Min Kim, Tae-Joon Jeon, Moon Ki Kim
Recently, the atomic structures of both the closed and open forms of Group 2 chaperonin protein Mm-cpn were revealed through crystallography and cryo-electron microscopy. This toroidal-like chaperonin is composed of two eightfold rings that face back-to-back. To gain a computational advantage, we used a symmetry constrained elastic network model (SCENM), which requires only a repeated subunit structure and its symmetric connectivity to neighboring subunits to simulate the entire system. In the case of chaperonin, only six subunits (i...
June 2014: Protein Science: a Publication of the Protein Society
Oksana A Sergeeva, Jingkun Yang, Jonathan A King, Kelly M Knee
The features in partially folded intermediates that allow the group II chaperonins to distinguish partially folded from native states remain unclear. The archaeal group II chaperonin from Methanococcus Mauripaludis (Mm-Cpn) assists the in vitro refolding of the well-characterized β-sheet lens protein human γD-crystallin (HγD-Crys). The domain interface and buried cores of this Greek key conformation include side chains, which might be exposed in partially folded intermediates. We sought to assess whether particular features buried in the native state, but absent from the native protein surface, might serve as recognition signals...
June 2014: Protein Science: a Publication of the Protein Society
Michael Vouche, Laura Kulik, Rohi Atassi, Khairuddin Memon, Ryan Hickey, Daniel Ganger, Frank H Miller, Vahid Yaghmai, Michael Abecassis, Talia Baker, Mary Mulcahy, Ritu Nayar, Robert J Lewandowski, Riad Salem
UNLABELLED: The aim of this study was to compare radiological and pathological changes and test the adjunct efficacy of Sorafenib to Y90 as a bridge to transplantation in hepatocellular carcinoma (HCC). 15 patients with 16 HCC lesions were randomized to Y90 without (Group A, n = 9) or with Sorafenib (Group B, n = 7). Size (WHO, RECIST), enhancement (EASL, mRECIST) and diffusion-weighted imaging criteria (apparent diffusion coefficient, ADC) measurements were obtained at baseline, then at 1 and every 3 months after treatment until transplantation...
November 2013: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
Sang-Eun Lee, Hyang-Yeol Lee, Kyung-Hwan Jung
We investigated the transgalactosylation reaction of chlorphenesin (CPN) using β-galactosidase (β-gal)-containing Escherichia coli (E. coli) cells, in which galactose from lactose was transferred to CPN. The optimal CPN concentration for CPN galactoside (CPN-G) synthesis was observed at 40 mM under the conditions that lactose and β-gal (as E. coli cells) were 400 g/l and 4.8 U/ml, respectively, and the pH and temperature were 7.0 and 40oC, respectively. The time-course profile of CPN-G synthesis under these optimal conditions showed that CPN-G synthesis from 40 mM CPN reached a maximum of about 27 mM at 12 h...
June 28, 2013: Journal of Microbiology and Biotechnology
Sang-Eun Lee, Tae-Min Jo, Hyang-Yeol Lee, Jongsung Lee, Kyung-Hwan Jung
We synthesized galactosyl chlorphenesin (CPN-G) using β-gal-containing Escherichia coli (E. coli) cells in which the conversion yield of chlorphenesin (CPN) to CPN-G reached about 64 % during 12 h. CPN-G was identified and characterized using high-performance liquid chromatography, liquid chromatography-mass spectrometry, Fourier transform-infrared spectrometry, and nuclear magnetic resonance analysis ((1)H and (13)C). We verified that a galactose was covalently bound to a CPN alcohol group during CPN-G synthesis throughout these analyses...
November 2013: Applied Biochemistry and Biotechnology
Hui Sun, Cong-Feng Luo, Guang Yang, Hui-Peng Shi, Bing-Fang Zeng
OBJECTIVE: The study was undertaken to evaluate the efficacy and safety of a posterolateral reversed L-shaped knee joint incision for treating the posterolateral tibial plateau fracture. METHODS: Knee specimens from eight fresh, frozen adult corpses were dissected bilaterally using a posterolateral reversed L-shaped approach. During the dissection, the exposure range was observed, and important parameters of anatomical structure were measured, including the parameters of common peroneal nerve (CPN) to ameliorate the incision and the distances between bifurcation of main vessels and the tibial articular surface to clear risk awareness...
October 2013: European Journal of Orthopaedic Surgery & Traumatology: Orthopédie Traumatologie
Keith R Willison
The ATP-dependence of folding chamber closure in the 16-subunit homo-oligomeric chaperonin from archaea Methanococcus maripaludis (Mm-cpn) has been studied by single particle cryo-electron microscopy (Zhang et al., 2011). ATP binding alone causes a rigid body rotation of ~45° and slight closure of the cavity, but full closure requires ATP hydrolysis.
June 8, 2011: Structure
Junjie Zhang, Boxue Ma, Frank DiMaio, Nicholai R Douglas, Lukasz A Joachimiak, David Baker, Judith Frydman, Michael Levitt, Wah Chiu
Chaperonins are large ATP-driven molecular machines that mediate cellular protein folding. Group II chaperonins use their "built-in lid" to close their central folding chamber. Here we report the structure of an archaeal group II chaperonin in its prehydrolysis ATP-bound state at subnanometer resolution using single particle cryo-electron microscopy (cryo-EM). Structural comparison of Mm-cpn in ATP-free, ATP-bound, and ATP-hydrolysis states reveals that ATP binding alone causes the chaperonin to close slightly with a ∼45° counterclockwise rotation of the apical domain...
May 11, 2011: Structure
Mohamad A Eloubeidi
BACKGROUND AND AIMS: A forward-viewing echoendoscope (FV-CLA) has been recently developed for performing interventional endoscopic ultrasound (EUS). The role of FV-CLA in performing standard EUS-guided fine-needle aspiration (FNA), Tru-cut biopsy (TCB), and celiac plexus neurolysis (CPN) is unknown. Our aims were to evaluate the feasibility of the FV-CLA for performing EUS-guided FNA/TCB and CPN. METHODS: In this prospective study conducted over a 3-month period, 30 patients were evaluated with the FV-CLA...
January 2011: Journal of Gastroenterology and Hepatology
Lars Karlsson, Martin Björck, Håkan Pärsson, Anders Wanhainen
BACKGROUND: To investigate the association between serological markers for Chlamydophila pneumoniae (Cpn) and the development of abdominal aortic aneurysm (AAA) in a population-based case-control study. METHODS: A screening for AAA among 65-75-year-old men and women was performed in a population with high prevalence of disease. Most of the subjects had undergone previous testing at the age of 60, including blood sampling. A total of 42 patients with AAA were compared with 100 age- and gender-matched controls with normal aortas...
April 2011: Annals of Vascular Surgery
Kelly M Knee, Daniel R Goulet, Junjie Zhang, Bo Chen, Wah Chiu, Jonathan A King
Chaperonins assist in the folding of nascent and misfolded proteins, though the mechanism of folding within the lumen of the chaperonin remains poorly understood. The archeal chaperonin from Methanococcus marapaludis, Mm-Cpn, shares the eightfold double barrel structure with other group II chaperonins, including the eukaryotic TRiC/CCT, required for actin and tubulin folding. However, Mm-Cpn is composed of a single species subunit, similar to group I chaperonin GroEL, rather than the eight subunit species needed for TRiC/CCT...
January 2011: Protein Science: a Publication of the Protein Society
Matthew L Baker, Mariah R Baker, Corey F Hryc, Frank Dimaio
Today, electron cryomicroscopy (cryo-EM) can routinely achieve subnanometer resolutions of complex macromolecular assemblies. From a density map, one can extract key structural and functional information using a variety of computational analysis tools. At subnanometer resolution, these tools make it possible to isolate individual subunits, identify secondary structures, and accurately fit atomic models. With several cryo-EM studies achieving resolutions beyond 5Å, computational modeling and feature recognition tools have been employed to construct backbone and atomic models of the protein components directly from a density map...
2010: Methods in Enzymology
Matthew L Baker, Junjie Zhang, Steven J Ludtke, Wah Chiu
With single-particle electron cryomicroscopy (cryo-EM), it is possible to visualize large, macromolecular assemblies in near-native states. Although subnanometer resolutions have been routinely achieved for many specimens, state of the art cryo-EM has pushed to near-atomic (3.3-4.6 Å) resolutions. At these resolutions, it is now possible to construct reliable atomic models directly from the cryo-EM density map. In this study, we describe our recently developed protocols for performing the three-dimensional reconstruction and modeling of Mm-cpn, a group II chaperonin, determined to 4...
September 2010: Nature Protocols
Junjie Zhang, Matthew L Baker, Gunnar F Schröder, Nicholai R Douglas, Stefanie Reissmann, Joanita Jakana, Matthew Dougherty, Caroline J Fu, Michael Levitt, Steven J Ludtke, Judith Frydman, Wah Chiu
Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states...
January 21, 2010: Nature
H A M Saleh, M M O El-fark, G A Abdel-Hamid
The sciatic nerve (SN) originates from the L4-S3 roots in the form of two nerve trunks: the tibial nerve (TN) and the common peroneal nerve (CPN). The TN and CPN are encompassed by a single epineural sheath and eventually separate (divide) in the popliteal fossa. This division of the SN occurs at a variable level above the knee and may account for frequent failures reported with the popliteal block. We studied the level of division of the SN in the popliteal fossa and its relationship to the common epineural sheath of the SN...
November 2009: Folia Morphologica (Warsz)
Lars Karlsson, Judy Gnarpe, David Bergqvist, Johan Lindbäck, Håkan Pärsson
OBJECTIVE: The aim of the study was to evaluate the effect of azithromycin on the expansion rate of small abdominal aortic aneurysms (AAAs), and to determine whether or not a correlation exists between serological markers for Chlamydophilia pneumonia (Cpn) infection and AAA expansion. METHODS: Nine vascular centers were included and 259 patients were invited to participate. Ten patients declined and 2 patients had chronic kidney failure, leaving a total of 247 patients...
July 2009: Journal of Vascular Surgery
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