Structure and function of cement proteins in human adenovirus

Human adenoviruses (HAdVs) are large (~150nm in diameter, 150MDa) nonenveloped double-stranded DNA (dsDNA) viruses that cause respiratory, ocular, and enteric diseases. The capsid shell of adenovirus (Ad) comprises multiple copies of three major capsid proteins (MCP: hexon, penton base and fiber) and four minor/cement proteins (IIIa, VI, VIII and IX) that are organized with pseudo T=25 icosahedral symmetry. In addition, six other proteins (V, VII, μ, IVa2, terminal protein and protease) are encapsidated along with the 36Kb dsDNA genome inside the capsid. The crystal structures of all three MCPs are known and so is their organization in the capsid from prior X-ray crystallography and cryoEM analyses. However structures and locations of various cement proteins are of considerable debate. We have determined and refined the structure of an entire human adenovirus employing X-ray crystallpgraphic methods at 3.8Å resolution. Adenovirus cement proteins play crucial roles in virion assembly, disassembly, cell entry and infection. Based on the refined crystal structure of adenovirus, we have determined the structure of the cement protein VI, a key membrane-lytic molecule and its associations with proteins V and VIII, which together glue peripentonal hexons beneath vertex region and connect them to rest of the capsid. Following virion maturation, the cleaved N-terminal pro-peptide of VI is observed deep in the peripentonal hexon cavity, detached from the membrane-lytic domain. Furthermore, we have significantly revised the recent cryoEM models for proteins IIIa and IX and both are located on the capsid exterior. Together, the cement proteins exclusively stabilize the hexon shell, thus rendering penton vertices the weakest links of the adenovirus capsid. Adenovirus cement protein structures reveal the molecular basis of the maturation cleavage of VI that is needed for endosome rupture and delivery of the virion into cytoplasm.

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Solving a new R2lox protein structure by microcrystal electron diffraction

Science Advances ◽

10.1126/sciadv.aax4621 ◽

2019 ◽

Vol 5 (8) ◽

pp. eaax4621 ◽

Cited By ~ 17

Author(s):

Hongyi Xu ◽

Hugo Lebrette ◽

Max T. B. Clabbers ◽

Jingjing Zhao ◽

Julia J. Griese ◽

...

Keyword(s):

Protein Structure ◽

Electron Diffraction ◽

Model Building ◽

Protein Structures ◽

X Ray Diffraction ◽

X Ray ◽

X Ray Crystallography ◽

Potential Map ◽

Metal Cofactor ◽

And Function

Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure—an R2lox enzyme—solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-Å resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.

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Solving the first novel protein structure by 3D micro-crystal electron diffraction

10.1101/600387 ◽

2019 ◽

Cited By ~ 1

Author(s):

H. Xu ◽

H. Lebrette ◽

M.T.B. Clabbers ◽

J. Zhao ◽

J.J. Griese ◽

...

Keyword(s):

Protein Structure ◽

Electron Diffraction ◽

Model Building ◽

Protein Structures ◽

X Ray ◽

X Ray Crystallography ◽

Unknown Protein ◽

Potential Map ◽

Crystal Electron ◽

And Function

AbstractMicro-crystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables studying biomolecules from micron-sized 3D crystals that are too small to be studied by conventional X-ray crystallography. However, to the best of our knowledge, MicroED has only been applied to re-determine protein structures that had already been solved previously by X-ray diffraction. Here we present the first unknown protein structure – an R2lox enzyme – solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0 Å resolution was of sufficient quality to allow accurate model building and refinement. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function, opening up new opportunities for structural biologists.

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Heavy Atom Detergent/Lipid Combined X-ray Crystallography for Elucidating the Structure-Function Relationships of Membrane Proteins

Membranes ◽

10.3390/membranes11110823 ◽

2021 ◽

Vol 11 (11) ◽

pp. 823

Author(s):

Shinya Hanashima ◽

Takanori Nakane ◽

Eiichi Mizohata

Keyword(s):

Membrane Proteins ◽

Structure Function ◽

New Technologies ◽

Heavy Atom ◽

Protein Structures ◽

X Ray ◽

X Ray Crystallography ◽

Function Relationship ◽

And Function ◽

Relationship Of

Membrane proteins reside in the lipid bilayer of biomembranes and the structure and function of these proteins are closely related to their interactions with lipid molecules. Structural analyses of interactions between membrane proteins and lipids or detergents that constitute biological or artificial model membranes are important for understanding the functions and physicochemical properties of membrane proteins and biomembranes. Determination of membrane protein structures is much more difficult when compared with that of soluble proteins, but the development of various new technologies has accelerated the elucidation of the structure-function relationship of membrane proteins. This review summarizes the development of heavy atom derivative detergents and lipids that can be used for structural analysis of membrane proteins and their interactions with detergents/lipids, including their application with X-ray free-electron laser crystallography.

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Beyond History: The List of The Most Well Studied Human Protein Structures

10.20944/preprints202008.0655.v1 ◽

2020 ◽

Author(s):

Zhenlu Li ◽

Matthias Buck

Keyword(s):

Protein Structures ◽

Protein Sequences ◽

Human Protein ◽

Current Status ◽

Protein Database ◽

X Ray ◽

X Ray Crystallography ◽

Protein Biophysics ◽

The Relationship ◽

Past Trend

Of 20,000 or so canonical human protein sequences, as of July 2020, 6,747 proteins have had their full or partial medium to high-resolution structures determined by x-ray crystallography or other methods. Which of these proteins dominate the protein database (the PDB) and why? In this paper, we list the 272 top protein structures based on the number of their PDB depositions. This set of proteins accounts for more than 40% of all available human PDB entries and represent past trend and current status for protein science. We briefly discuss the relationship which some of the prominent protein structures have with protein biophysics research and mention their relevance to human diseases. The information may inspire researchers who are new to protein science, but it also provides a year 2020 snap-shot for the state of protein science.

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Methods for Determining and Understanding Serpin Structure and Function: X-Ray Crystallography

Methods in Molecular Biology - Serpins ◽

10.1007/978-1-4939-8645-3_2 ◽

2018 ◽

pp. 9-39

Author(s):

Brian P. Mahon ◽

Robert McKenna

Keyword(s):

Structure And Function ◽

X Ray ◽

X Ray Crystallography ◽

And Function

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Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

International Journal of Molecular Sciences ◽

10.3390/ijms19113401 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3401 ◽

Cited By ~ 16

Author(s):

Ashutosh Srivastava ◽

Tetsuro Nagai ◽

Arpita Srivastava ◽

Osamu Miyashita ◽

Florence Tama

Keyword(s):

Protein Dynamics ◽

Computational Methods ◽

Protein Structures ◽

Three Dimensional ◽

Dimensional Structure ◽

X Ray ◽

X Ray Crystallography ◽

Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

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Structural and mechanistic bases for a potent HIV-1 capsid inhibitor

Science ◽

10.1126/science.abb4808 ◽

2020 ◽

Vol 370 (6514) ◽

pp. 360-364 ◽

Cited By ~ 10

Author(s):

Stephanie M. Bester ◽

Guochao Wei ◽

Haiyan Zhao ◽

Daniel Adu-Ampratwum ◽

Naseer Iqbal ◽

...

Keyword(s):

Principal Component ◽

X Ray ◽

X Ray Crystallography ◽

Cryo Electron Microscopy ◽

Capsid Shell ◽

Hydrogen Deuterium ◽

Infected Cells ◽

Long Acting ◽

Structural Insights ◽

Hiv 1

The potent HIV-1 capsid inhibitor GS-6207 is an investigational principal component of long-acting antiretroviral therapy. We found that GS-6207 inhibits HIV-1 by stabilizing and thereby preventing functional disassembly of the capsid shell in infected cells. X-ray crystallography, cryo–electron microscopy, and hydrogen-deuterium exchange experiments revealed that GS-6207 tightly binds two adjoining capsid subunits and promotes distal intra- and inter-hexamer interactions that stabilize the curved capsid lattice. In addition, GS-6207 interferes with capsid binding to the cellular HIV-1 cofactors Nup153 and CPSF6 that mediate viral nuclear import and direct integration into gene-rich regions of chromatin. These findings elucidate structural insights into the multimodal, potent antiviral activity of GS-6207 and provide a means for rationally developing second-generation therapies.

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General discussion summary

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2002.1149 ◽

2002 ◽

Vol 357 (1426) ◽

pp. 1419-1420 ◽

Cited By ~ 2

Keyword(s):

Water Splitting ◽

Molecular Mechanisms ◽

Structure And Function ◽

X Ray ◽

X Ray Crystallography ◽

And Function ◽

Splitting Process

This general discussion was chaired by A. W. Rutherford ( Service de Bioénergétique, Saclay, France ) and revolved around two major topics: (i) the implications of X–ray crystallography on the relationships between structure and function; (ii) the molecular mechanisms of the water–splitting process.

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