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How to Avoid the Travails of a Research Manager (or the Pitfall of Ending Up Not Doing Science)
Published in John R. Helliwell, Skills for a Scientific Life, 2016
In a second domain of retraining in my sabbatical, with my freedom of time and free of regular work commitments, I set about refreshing my core expertise in calculations. In my field, a key annual school/training/conference event is the CCP4* protein crystallography study weekend. I started reattending these; the first one happened to be very timely being in the first few months of my sabbatical. I felt slightly guilty taking up a place that might have been occupied by a PhD student, but no one commented. But anyway, quite a core of experienced people besides the invited speakers and the large number of students do attend these study weekends.
Molecular recognition requires dimerization of a VHH antibody
Published in mAbs, 2023
Christopher A. Smith, Gregory J. Sonneson, Robert J. Hoey, Jennifer M. Hinerman, Kimberly Sheehy, Richard Walter, Andrew B. Herr, James R. Horn
Molecular replacement was performed using the program MOLREP and the anti-RNaseA VHH domain from PDB accession code 1BZQ (chain K) serving as the search model.5 Initial rounds of molecular replacement generated a dimeric model which was used in subsequent molecular replacement searches which ultimately identified a unit cell containing four dimer complexes. Initial refinements to the data were done with the Refmac/CCP4 program suite34 and then using Phenix.35 Model adjustments between refinements were performed using Coot.36 The structure was deposited in the Protein Data Base (PDB ID: 8FTG). Available surface area calculations were performed using the program NACCESS.37 Buried surface area calculations were carried out by comparing the surface area of each residue to an Ala-X-Ala tripeptide.
Short divalent ethacrynic amides as pro-inhibitors of glutathione S-transferase isozyme Mu and potent sensitisers of cisplatin-resistant ovarian cancers
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2022
Bangtian Xu, Tingting Tong, Xin Wang, Fang Liu, Xiang Zhang, Xiaolei Hu, Xinpeng Li, Xiaolan Yang, Fei Liao
Diffraction data were collected at beamline BL17U of Shanghai Synchrotron Radiation Facility (SSRF, Shanghai, China) at 100 K and a wavelength of 0.97915 Å. The data were indexed and scaled by IMOSFLM and SCALA as implemented in CCP4 (Collaborative Computational Project, number 4), respectively40. The crystals belonged to the space group P1211 and diffracted to 1.6 Å. Using PDB accession code 1XW5 of human GSTM as the search model, initial phases were determined by molecular replacement with as-implemented program in CCP4 suite41. Cycles of manual adjustment using Coot and subsequent refinement using PHENIX led to a final model with a R factor (Rcryst) of 17.92% and a free R factor (Rfree) of 20.55% at 1.60 Å resolution42,43. Crystal property data were collected in Supplementary Note S1-Table S1, and the structure model was deposited in PDB with the accession code of 5HWL.
A strategy for the efficient construction of anti-PD1-based bispecific antibodies with desired IgG-like properties
Published in mAbs, 2022
Jie Zhao, Liangfeng Jiang, Haodong Yang, Lan Deng, Xiaoqing Meng, Jian Ding, Sixing Yang, Le Zhao, Wei Xu, Xiaolong Wang, Zhenping Zhu, Haomin Huang
Diffraction images were collected at the Shanghai Synchrotron Radiation Facility (SSRF), beamline BL18U1. Raw images were collected through a Pilatus detector and were indexed, integrated and scaled using XDS. All diffraction experiments were carried out at 100 K. Data were collected at a wavelength of 0.97915 Å for PD1/609A-Fab complexes. Resolution limits were cut off at I/σ(I) = 2.2. Phase was determined by molecular replacement with Phaser using the human PD1 structure (PDB ID: 5WT9) and the nivolumab/Fab structure (PDB ID: 5WT9) as search ensembles (models). Structure refinement was carried out using Refmac5. Structure inspection, building, and validation were performed by COOT. Analysis for interaction within complexes was carried out by ccp4.PISA, and figures were generated using PyMOL. The atomic coordinates and sequences of the PD1/609A-Fab complex have been deposited in the Protein Data Bank with an accession code of 7VUX.