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      Vasoinhibin comprises a three-helix bundle and its antiangiogenic domain is located within the first 79 residues

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          Abstract

          Vasoinhibin belongs to a family of angiogenesis inhibitors generated when the fourth α-helix (H4) of the hormone prolactin (PRL) is removed by specific proteolytic cleavage. The antiangiogenic properties are absent in uncleaved PRL, indicating that conformational changes create a new bioactive domain. However, the solution structure of vasoinhibin and the location of its bioactive domain are unknown. Molecular dynamic simulation (MD) showed that the loss of H4 exposes the hydrophobic nucleus of PRL and leads to the compression of the molecule into a three-helix bundle that buries the hydrophobic nucleus again. Compression occurs by the movement of loop 1 (L1) and its interaction with α-helix 1 (H1) generating a new L1 conformation with electrostatic and hydrophobic surfaces distinct from those of PRL, that may correspond to a bioactive domain. Consistent with this model, a recombinant protein containing the first 79 amino acids comprising H1 and L1 of human PRL inhibited the proliferation and migration of endothelial cells and upregulated the vasoinhibin target genes, IL1A and ICAM1. This bioactivity was comparable to that of a conventional vasoinhibin having the 123 residues encompassing H1, L1, Η2, L2, and Η3 of human PRL. These findings extend the vasoinhibin family to smaller proteins and provide important structural information, which will aid in antiangiogenic drug development.

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          Most cited references52

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          Tricine-SDS-PAGE.

          Tricine-SDS-PAGE is commonly used to separate proteins in the mass range 1-100 kDa. It is the preferred electrophoretic system for the resolution of proteins smaller than 30 kDa. The concentrations of acrylamide used in the gels are lower than in other electrophoretic systems. These lower concentrations facilitate electroblotting, which is particularly crucial for hydrophobic proteins. Tricine-SDS-PAGE is also used preferentially for doubled SDS-PAGE (dSDS-PAGE), a proteomic tool used to isolate extremely hydrophobic proteins for mass spectrometric identification, and it offers advantages for resolution of the second dimension after blue-native PAGE (BN-PAGE) and clear-native PAGE (CN-PAGE). Here I describe a protocol for Tricine-SDS-PAGE, which includes efficient methods for Coomassie blue or silver staining and electroblotting, thereby increasing the versatility of the approach. This protocol can be completed in 1-2 d.
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            A chemical method for fast and sensitive detection of DNA synthesis in vivo.

            We have developed a method to detect DNA synthesis in proliferating cells, based on the incorporation of 5-ethynyl-2'-deoxyuridine (EdU) and its subsequent detection by a fluorescent azide through a Cu(I)-catalyzed [3 + 2] cycloaddition reaction ("click" chemistry). Detection of the EdU label is highly sensitive and can be accomplished in minutes. The small size of the fluorescent azides used for detection results in a high degree of specimen penetration, allowing the staining of whole-mount preparations of large tissue and organ explants. In contrast to BrdU, the method does not require sample fixation or DNA denaturation and permits good structural preservation. We demonstrate the use of the method in cultured cells and in the intestine and brain of whole animals.
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              Is Open Access

              H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

              The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.
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                Author and article information

                Contributors
                clapp@unam.mx
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                20 November 2018
                20 November 2018
                2018
                : 8
                : 17111
                Affiliations
                [1 ]ISNI 0000 0001 2159 0001, GRID grid.9486.3, Instituto de Neurobiología, , Universidad Nacional Autónoma de México (UNAM), ; Querétaro, Mexico
                [2 ]ISNI 0000 0001 2159 0001, GRID grid.9486.3, Biofísica y Ciencia de Materiales, , Instituto de Ciencias Físicas, UNAM, ; Cuernavaca, Mexico
                [3 ]Institute for Clinical Chemistry, Laboratory Medicine and Transfusion Medicine, Nuremberg General Hospital & Paracelsus Medical University, Nuremberg, Germany
                Author information
                http://orcid.org/0000-0002-4407-9828
                http://orcid.org/0000-0002-1989-8645
                Article
                35383
                10.1038/s41598-018-35383-7
                6244167
                30459448
                772ebd24-e914-4f77-b6a6-c9a1b01944fc
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 25 June 2018
                : 1 November 2018
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100003141, Consejo Nacional de Ciencia y Tecnología (National Council of Science and Technology, Mexico);
                Award ID: 394345 fellowship
                Award ID: 220574
                Award ID: 394345 fellowship
                Award ID: 220574
                Award ID: 394345 fellowship
                Award ID: 394345 fellowship
                Award ID: 220574
                Award ID: 394345 fellowship
                Award ID: 220574
                Award ID: 394345 fellowship
                Award ID: 220574
                Award ID: 220574
                Award ID: 394345 fellowship
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100005739, Universidad Nacional Autónoma de México (UNAM);
                Award ID: UR405-PC
                Award Recipient :
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