An Iterative Direct Phasing Algorithm for Protein Structure Determination

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dc.contributor.advisorSu, Wu-Pei
dc.contributor.committeeMemberGunaratne, Gemunu H.
dc.contributor.committeeMemberJackson, David R.
dc.contributor.committeeMemberLi, Liming
dc.contributor.committeeMemberMiller, John H., Jr.
dc.creatorJiang, Mengchao 1991-
dc.date.accessioned2019-12-17T20:06:21Z
dc.date.createdDecember 2019
dc.date.issued2019-12
dc.date.submittedDecember 2019
dc.date.updated2019-12-17T20:06:22Z
dc.description.abstractAn iterative phasing method based on the hybrid input-output (HIO) algorithm, proposed by He & Su (2015), is improved to retrieve phases of protein crystals. By testing the method on a protein crystal with 65% solvent content, it is proved that this method is capable of phasing protein crystals with an intermediate solvent content. Results from a blind test have yielded an interpretable density map, which shows that the phasing method is capable of solving completely unknown protein structures. The phasing method was tested on medium- and low-resolution diffraction data of a membrane protein, which shows that the atomic structure can be solved directly from the diffraction data with resolution higher than 3.5Å. For data of lower resolutions, secondary structures and the protein boundary can still be obtained. The results also indicate that there is an optimal histogram to use for data at various resolutions. By averaging over tens of successful runs, the resulting density map can be greatly improved and the final phase error can be reduced by about 10 degrees, thus leading to a better reconstructed model. Finally, a density constraint called non-crystallographic symmetry (NCS) is employed to overcome the undersampling condition of protein crystals with low solvent content. The phasing method has been applied to a protein crystal with 3-fold rotational NCS and 45% solvent content. The results show that, when the NCS axis is well positioned, the protein envelope and the NCS mask can be automatically rebuilt. By employing NCS averaging, this method is thus capable of solving protein crystals with low solvent content.
dc.description.departmentPhysics, Department of
dc.format.digitalOriginborn digital
dc.format.mimetypeapplication/pdf
dc.identifier.citationPortions of this document appear in: Jiang, Mengchao, Hongxing He, and Wu-Pei Su. "Trial Direct Phasing Calculation of A Thyroid Hormone Receptor Alpha Structure (4LNW)." Crystals 9, no. 10 (2019): 533. And in: Jiang, Mengchao, Hongxing He, Yunpeng Cheng, and Wu-Pei Su. "Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray Crystallography." Crystals 8, no. 4 (2018): 156. And in: He, Hongxing, Mengchao Jiang, and Wu-Pei Su. "Direct Phasing of Protein Crystals with Non-Crystallographic Symmetry." Crystals 9, no. 1 (2019): 55.
dc.identifier.urihttps://hdl.handle.net/10657/5594
dc.language.isoeng
dc.rightsThe author of this work is the copyright owner. UH Libraries and the Texas Digital Library have their permission to store and provide access to this work. UH Libraries has secured permission to reproduce any and all previously published materials contained in the work. Further transmission, reproduction, or presentation of this work is prohibited except with permission of the author(s).
dc.subjectX-ray crystallography
dc.subjectHybrid input-output
dc.subjectIterative direct phasing method
dc.subjectAb initio phasing
dc.subjectNon-crystallographic symmetry
dc.titleAn Iterative Direct Phasing Algorithm for Protein Structure Determination
dc.type.dcmiText
dc.type.genreThesis
local.embargo.lift2021-12-01
local.embargo.terms2021-12-01
thesis.degree.collegeCollege of Natural Sciences and Mathematics
thesis.degree.departmentPhysics, Department of
thesis.degree.disciplinePhysics
thesis.degree.grantorUniversity of Houston
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy

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