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      Comparative studies of the expression of creatine kinase isoforms under immune stress in Pelodiscus sinensis

      research-article
      a , 1 , a , 1 , b , a , a , a , a , c , * , a , **
      International Journal of Biological Macromolecules
      Elsevier B.V.
      CK, creatine kinase, PSCK, CK from Pelodiscus sinensis, PSCK-B, brain type of PSCK, PSCK-M, muscle type of PSCK, PSCK-S, mitochondrial sarcomeric type of PSCK (type II), ADP, adenosine diphosphate, ATP, adenosine triphosphate, MD, molecular dynamics, ps, picosecond, ns, nanosecond, T-SOD, total superoxide dismutase, LDH, lactate dehydrogenase, MDA, malondialdehyde, CAT, catalase, IHC, immunohistochemistry, RT-PCR, reverse transcription polymerase chain reaction, RACE, rapid-amplification of cDNA ends, Creatine kinase, Pelodiscus sinensis, Immune stress

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          Abstract

          The expression and localization of different isoforms of creatine kinase in Pelodiscus sinensis (PSCK) were studied to reveal the role of PSCK isozymes (PSCK-B, PSCK-M, PSCK-S) under bacterial infection-induced immunologic stress. The computational molecular dynamics simulations predicted that PSCK-S would mostly possess a kinase function in a structural aspect when compared to PSCK-B and PSCK-M. The assay of biochemical parameters such as total superoxide dismutase (T-SOD), lactate dehydrogenase (LDH), malondialdehyde (MDA), catalase (CAT), and the content of ATP were measured along with total PSCK activity in different tissue samples under bacterial infection. The expression detections of PSCK isozymes in vitro and in vivo were overall well-matched where PSCK isozymes were expressed differently in P. sinensis tissues. The results showed that PSCK-B mostly contributes to the spleen, followed by the liver and myocardium; PSCK-M mostly contributes to the liver, followed by the myocardium and skeletal muscle, while PSCK-S contributes to the spleen and is uniquely expressed in skeletal muscle. Our study suggests that the various alterations of PSCK isozymes in tissues of P. sinensis are prone to defense the bacterial infection and blocking energetic imbalance before severe pathogenesis turned on in P. sinensis.

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          Most cited references26

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          CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. 2008 Wiley Periodicals, Inc.
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            Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution. We have generalized the alignment of protein sequences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile HMMs. We present a method for detecting distant homologous relationships between proteins based on this approach. The method (HHsearch) is benchmarked together with BLAST, PSI-BLAST, HMMER and the profile-profile comparison tools PROF_SIM and COMPASS, in an all-against-all comparison of a database of 3691 protein domains from SCOP 1.63 with pairwise sequence identities below 20%.Sensitivity: When the predicted secondary structure is included in the HMMs, HHsearch is able to detect between 2.7 and 4.2 times more homologs than PSI-BLAST or HMMER and between 1.44 and 1.9 times more than COMPASS or PROF_SIM for a rate of false positives of 10%. Approximately half of the improvement over the profile-profile comparison methods is attributable to the use of profile HMMs in place of simple profiles. Alignment quality: Higher sensitivity is mirrored by an increased alignment quality. HHsearch produced 1.2, 1.7 and 3.3 times more good alignments ('balanced' score >0.3) than the next best method (COMPASS), and 1.6, 2.9 and 9.4 times more than PSI-BLAST, at the family, superfamily and fold level, respectively.Speed: HHsearch scans a query of 200 residues against 3691 domains in 33 s on an AMD64 2GHz PC. This is 10 times faster than PROF_SIM and 17 times faster than COMPASS.
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              Based on recent developments in generalized Born (GB) theory that employ rapid volume integration schemes (M. S. Lee, F. R. Salabury, Jr., and C. L. Brooks III, J Chem Phys 2002, 116, 10606) we have recast the calculation of the self-electrostatic solvation energy to utilize a simple smoothing function at the dielectric boundary. The present GB model is formulated in this manner to provide consistency with the Poisson-Boltzmann (PB) theory previously developed to yield numerically stable electrostatic solvation forces based on finite-difference methods (W. Im, D. Beglov, and B. Roux, Comp Phys Commun 1998, 111, 59). Our comparisons show that the present GB model is indeed an efficient and accurate approach to reproduce corresponding PB solvation energies and forces. With only two adjustable parameters--a(0) to modulate the Coulomb field term, and a(1) to include a correction term beyond Coulomb field--the PB solvation energies are reproduced within 1% error on average for a variety of proteins. Detailed analysis shows that the PB energy can be reproduced within 2% absolute error with a confidence of about 95%. In addition, the solvent-exposed surface area of a biomolecule, as commonly used in calculations of the nonpolar solvation energy, can be calculated accurately and efficiently using the simple smoothing function and the volume integration method. Our implicit solvent GB calculations are about 4.5 times slower than the corresponding vacuum calculations. Using the simple smoothing function makes the present GB model roughly three times faster than GB models, which attempt to mimic the Lee-Richards molecular volume. Copyright 2003 Wiley Periodicals, Inc.
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                Author and article information

                Contributors
                Journal
                Int J Biol Macromol
                Int. J. Biol. Macromol
                International Journal of Biological Macromolecules
                Elsevier B.V.
                0141-8130
                1879-0003
                9 June 2020
                9 June 2020
                Affiliations
                [a ]College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
                [b ]Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
                [c ]Skin Diseases Research Center, Yangtze Delta Region Institute of Tsinghua University, 705 Yatai Road, Jiaxing 314006, PR China
                Author notes
                [* ]Correspondence to: Y-D. Park, B-18F, No. 705 Yatai Road, Nanhu District, Jiaxing 314006, Zhejiang, PR China. parkyd@ 123456hotmail.com
                [** ]Correspondence to: G-Y. Qian, No. 8 Qianhu South Road, Yinzhou District, Ningbo 315100, Zhejiang, PR China. qianguoying_wanli@ 123456hotmail.com
                [1]

                These authors contributed equally to this study.

                Article
                S0141-8130(20)33476-0
                10.1016/j.ijbiomac.2020.06.036
                7282771
                d15f1035-e85c-422b-8715-12a74da82660
                © 2020 Elsevier B.V. All rights reserved.

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                : 15 May 2020
                : 4 June 2020
                : 4 June 2020
                Categories
                Article

                Biochemistry
                ck, creatine kinase,psck, ck from pelodiscus sinensis,psck-b, brain type of psck,psck-m, muscle type of psck,psck-s, mitochondrial sarcomeric type of psck (type ii),adp, adenosine diphosphate,atp, adenosine triphosphate,md, molecular dynamics,ps, picosecond,ns, nanosecond,t-sod, total superoxide dismutase,ldh, lactate dehydrogenase,mda, malondialdehyde,cat, catalase,ihc, immunohistochemistry,rt-pcr, reverse transcription polymerase chain reaction,race, rapid-amplification of cdna ends,creatine kinase,pelodiscus sinensis,immune stress

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