Jennifer Miao - Academia.edu (original) (raw)

Papers by Jennifer Miao

PDB-101: Learn: Guide to Understanding PDB Data: Methods ISIS Neutron diffractionElectron Diffrac... more PDB-101: Learn: Guide to Understanding PDB Data: Methods ISIS Neutron diffractionElectron Diffraction and Crystal StructureRCSB PDB 1IEP: CRYSTAL STRUCTURE OF THE C-ABL KINASE X-ray crystallography WikipediaChapter 3 X-ray diffraction � Bragg’s law � Laue’s Electron diffraction WikipediaEnhanced electron extraction using SnO2 for high X-Ray Diffraction an overview | ScienceDirect TopicsElectron Diffraction Boston UniversityCombined Approach of Mechanochemistry and Electron Crystal Structure Basic ConceptsRCSB PDB 3CIG: Crystal structure of mouse TLR3 ectodomainXRD BasicsAmerican Mineralogist Papers in PressElectron Backscatter Diffraction (EBSD)Laue Diffraction | PhysicsOpenLabTransmission Electron Microscopy an overview x Ray crystallographySingle Crystal and Powder X-ray Diffraction | ProtocolSilicon & Germanium Crystal Structure | PhysicsOpenLabELDICO Scientific AG HomeCrystal structure of oxygen-evolving photosystem II at a

Acta Crystallographica Section D Structural Biology, 2020

Structure determination of novel biological macromolecules by X-ray crystallography can be facili... more Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyala...

Acta Crystallographica Section A Foundations and Advances, 2019

The proof of principle of protein structure determination using MicroED (micro electron diffracti... more The proof of principle of protein structure determination using MicroED (micro electron diffraction) from submicron sized 2D protein crystals was established with lysozyme in 2013, for which molecular replacement (MR) was performed for phasing. Since that milestone, a number of different cases with resolution ranging from 3.2-1.0 Å have been solved. For atomic resolution, ab-initio methods, relying only on the measured intensities, were used for phasing. For lower resolutions, MR has been the phasing method of choice, but it requires a model. ARCIMBOLDO performs fragment-based MR with PHASER, using as models either secondary structure elements, or libraries of small local folds or fragments from a distant homolog. Such small accurate fragments produce many solutions from which only a few are correct, but density modification and mainchain autotracing with SHELXE allows the completion and discrimination of correct substructures. For non-atomic resolutions but better than 3 Å, this method has been successful in many X-ray structure determinations. Recently, we are adapting ARCIMBOLDO to work with electron scattering factors and using our model fragments, a number of MicroED datasets can be solved. In this work we will discuss the results of these cases and the current and future developments in our software for dealing with MicroED data.

The ice nucleation protein InaZ of Pseudomonas syringae contains a large number of degenerate rep... more The ice nucleation protein InaZ of Pseudomonas syringae contains a large number of degenerate repeats that span more than a quarter of its sequence and include the segment GSTSTA. We determine ab initio structures of this repeat segment, resolved to 1.1Å by microfocus x-ray crystallography and 0.9Å by the cryoEM method MicroED, from both racemic and homochiral crystals. We evaluate the benefits of racemic protein crystals for structure determination by MicroED and confirm that phase restriction introduced by crystal centrosymmetry increases the number of successful trials during ab initio phasing of electron diffraction data. Both homochiral and racemic GSTSTA form amyloid-like protofibrils with labile, corrugated antiparallel beta sheets that mate face to back. The racemic GSTSTA protofibril represents a new class of amyloid assembly in which all left-handed sheets mate with their all right-handed counterparts. Our determination of racemic amyloid assemblies by MicroED reveals comp...

Nature structural & molecular biology, Jan 15, 2018

The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian ... more The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'.

Theoretical calculations suggest that crystals exceeding 100 nm thickness are excluded by dynamic... more Theoretical calculations suggest that crystals exceeding 100 nm thickness are excluded by dynamical scattering from successful structure determination using microcrystal electron diffraction (MicroED). These calculations are at odds with experimental results where MicroED structures have been determined from significantly thicker crystals. Here we systematically evaluate the influence of thickness on the accuracy of MicroED intensities and the ability to determine structures from protein crystals one micrometer thick. To do so, we compare ab initio structures of a human prion protein segment determined from thin crystals to those determined from crystals up to one micrometer thick. We also compare molecular replacement solutions from crystals of varying thickness for a larger globular protein, proteinase K. Our results indicate that structures can be reliably determined from crystals at least an order of magnitude thicker than previously suggested by simulation, opening the possibil...

Frontiers in Neuroscience

Sequence variation in the β2α2 loop, residues 165-175 of the mammalian prion protein (PrP), influ... more Sequence variation in the β2α2 loop, residues 165-175 of the mammalian prion protein (PrP), influences its structure. To better understand the consequences of sequence variation in this region of the protein, we biochemically and biophysically interrogate natural and artificial sequence variants of the β2α2 loop of mammalian PrP. Using microcrystal electron diffraction (MicroED), we determine atomic resolution structures of segments encompassing residues 168-176 from the β2α2 loop of PrP with sequences corresponding to human, mouse/cow, bank vole/hamster, rabbit/pig/guinea pig, and naked mole rat (elk-T174S) β2α2 loops, as well as synthetic β2α2 loop sequences. This collection of structures presents two dominant amyloid packing polymorphisms. In the first polymorph, denoted “clasped”, side chains within a sheet form polar clasps by facing each other on the same strand, exemplified by the mouse/cow, human, and bank vole/hamster sequences. Because its stability is derived from within ...

PDB-101: Learn: Guide to Understanding PDB Data: Methods ISIS Neutron diffractionElectron Diffrac... more PDB-101: Learn: Guide to Understanding PDB Data: Methods ISIS Neutron diffractionElectron Diffraction and Crystal StructureRCSB PDB 1IEP: CRYSTAL STRUCTURE OF THE C-ABL KINASE X-ray crystallography WikipediaChapter 3 X-ray diffraction � Bragg’s law � Laue’s Electron diffraction WikipediaEnhanced electron extraction using SnO2 for high X-Ray Diffraction an overview | ScienceDirect TopicsElectron Diffraction Boston UniversityCombined Approach of Mechanochemistry and Electron Crystal Structure Basic ConceptsRCSB PDB 3CIG: Crystal structure of mouse TLR3 ectodomainXRD BasicsAmerican Mineralogist Papers in PressElectron Backscatter Diffraction (EBSD)Laue Diffraction | PhysicsOpenLabTransmission Electron Microscopy an overview x Ray crystallographySingle Crystal and Powder X-ray Diffraction | ProtocolSilicon & Germanium Crystal Structure | PhysicsOpenLabELDICO Scientific AG HomeCrystal structure of oxygen-evolving photosystem II at a

Acta Crystallographica Section D Structural Biology, 2020

Structure determination of novel biological macromolecules by X-ray crystallography can be facili... more Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyala...

Acta Crystallographica Section A Foundations and Advances, 2019

The proof of principle of protein structure determination using MicroED (micro electron diffracti... more The proof of principle of protein structure determination using MicroED (micro electron diffraction) from submicron sized 2D protein crystals was established with lysozyme in 2013, for which molecular replacement (MR) was performed for phasing. Since that milestone, a number of different cases with resolution ranging from 3.2-1.0 Å have been solved. For atomic resolution, ab-initio methods, relying only on the measured intensities, were used for phasing. For lower resolutions, MR has been the phasing method of choice, but it requires a model. ARCIMBOLDO performs fragment-based MR with PHASER, using as models either secondary structure elements, or libraries of small local folds or fragments from a distant homolog. Such small accurate fragments produce many solutions from which only a few are correct, but density modification and mainchain autotracing with SHELXE allows the completion and discrimination of correct substructures. For non-atomic resolutions but better than 3 Å, this method has been successful in many X-ray structure determinations. Recently, we are adapting ARCIMBOLDO to work with electron scattering factors and using our model fragments, a number of MicroED datasets can be solved. In this work we will discuss the results of these cases and the current and future developments in our software for dealing with MicroED data.

The ice nucleation protein InaZ of Pseudomonas syringae contains a large number of degenerate rep... more The ice nucleation protein InaZ of Pseudomonas syringae contains a large number of degenerate repeats that span more than a quarter of its sequence and include the segment GSTSTA. We determine ab initio structures of this repeat segment, resolved to 1.1Å by microfocus x-ray crystallography and 0.9Å by the cryoEM method MicroED, from both racemic and homochiral crystals. We evaluate the benefits of racemic protein crystals for structure determination by MicroED and confirm that phase restriction introduced by crystal centrosymmetry increases the number of successful trials during ab initio phasing of electron diffraction data. Both homochiral and racemic GSTSTA form amyloid-like protofibrils with labile, corrugated antiparallel beta sheets that mate face to back. The racemic GSTSTA protofibril represents a new class of amyloid assembly in which all left-handed sheets mate with their all right-handed counterparts. Our determination of racemic amyloid assemblies by MicroED reveals comp...

Nature structural & molecular biology, Jan 15, 2018

The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian ... more The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'.

Theoretical calculations suggest that crystals exceeding 100 nm thickness are excluded by dynamic... more Theoretical calculations suggest that crystals exceeding 100 nm thickness are excluded by dynamical scattering from successful structure determination using microcrystal electron diffraction (MicroED). These calculations are at odds with experimental results where MicroED structures have been determined from significantly thicker crystals. Here we systematically evaluate the influence of thickness on the accuracy of MicroED intensities and the ability to determine structures from protein crystals one micrometer thick. To do so, we compare ab initio structures of a human prion protein segment determined from thin crystals to those determined from crystals up to one micrometer thick. We also compare molecular replacement solutions from crystals of varying thickness for a larger globular protein, proteinase K. Our results indicate that structures can be reliably determined from crystals at least an order of magnitude thicker than previously suggested by simulation, opening the possibil...

Frontiers in Neuroscience

Sequence variation in the β2α2 loop, residues 165-175 of the mammalian prion protein (PrP), influ... more Sequence variation in the β2α2 loop, residues 165-175 of the mammalian prion protein (PrP), influences its structure. To better understand the consequences of sequence variation in this region of the protein, we biochemically and biophysically interrogate natural and artificial sequence variants of the β2α2 loop of mammalian PrP. Using microcrystal electron diffraction (MicroED), we determine atomic resolution structures of segments encompassing residues 168-176 from the β2α2 loop of PrP with sequences corresponding to human, mouse/cow, bank vole/hamster, rabbit/pig/guinea pig, and naked mole rat (elk-T174S) β2α2 loops, as well as synthetic β2α2 loop sequences. This collection of structures presents two dominant amyloid packing polymorphisms. In the first polymorph, denoted “clasped”, side chains within a sheet form polar clasps by facing each other on the same strand, exemplified by the mouse/cow, human, and bank vole/hamster sequences. Because its stability is derived from within ...