Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations

Journal Article · · Journal of Biological Chemistry
Nonsynonymous gene mutations can be beneficial, neutral, or detrimental to the stability, structure, and biological function of the encoded protein, but the effects of these mutations are often not readily predictable. For example, the β-propeller olfactomedin domain of myocilin (mOLF) exhibits a complex interrelationship among structure(s), stability, and aggregation. Numerous mutations within mOLF are linked to glaucoma; the resulting variants are less stable, aggregation-prone, and sequestered intracellularly, causing cytotoxicity. In this study, we report the first stable mOLF variants carrying substitutions in the calcium-binding site that exhibit solution characteristics indistinguishable from those of glaucoma variants. Crystal structures of these stable variants at 1.8–2.0-Å resolution revealed features that we could not predict by molecular dynamics simulations, including loss of loop structure, helix unwinding, and a blade shift. Double mutants that combined a stabilizing substitution and a selected glaucoma-causing single-point mutant rescued in vitro folding and stability defects. In the context of full-length myocilin, secretion of stable single variants was indistinguishable from that of the WT protein, and the double mutants were secreted to varying extents. In summary, our finding that mOLF can tolerate particular substitutions that render the protein stable despite a conformational switch emphasizes the complexities in differentiating between benign and glaucoma-causing variants and provides new insight into the possible biological function of myocilin.
Research Organization:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
National Institutes of Health (NIH); USDOE
OSTI ID:
1562708
Journal Information:
Journal of Biological Chemistry, Journal Name: Journal of Biological Chemistry Journal Issue: 34 Vol. 294; ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular BiologyCopyright Statement
Country of Publication:
United States
Language:
ENGLISH

References (79)

Scalable molecular dynamics with NAMD journal January 2005
NMRPipe: A multidimensional spectral processing system based on UNIX pipes journal November 1995
Olfactomedin domain-containing proteins: evolution, functional divergence, expression patterns and damaging SNPs journal March 2019
Improving the specificity of organophosphorus hydrolase to acephate by mutagenesis at its binding site: a computational study journal May 2021
VMD: Visual molecular dynamics journal February 1996
Evolution of an Antibiotic Resistance Enzyme Constrained by Stability and Activity Trade-offs journal June 2002
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997
Stability and function: two constraints in the evolution of barstar and other proteins journal October 1994
Reversal of mutant myocilin non-secretion and cell killing: Implications for glaucoma journal February 2005
Accumulation of mutant myocilins in ER leads to ER stress and potential cytotoxicity in human trabecular meshwork cells journal December 2003
In vivo folding efficiencies for mutants of the P22 tailspike β-helix protein correlate with predicted stability changes journal May 2009
Temperature sensitive secretion of mutant myocilins journal June 2006
Mutant human myocilin induces strain specific differences in ocular hypertension and optic nerve damage in mice journal July 2012
Targeting the ER-autophagy system in the trabecular meshwork to treat glaucoma journal March 2016
Elucidation of subfamily segregation and intramolecular coevolution of the olfactomedin-like proteins by comprehensive phylogenetic analysis and gene expression pattern assessment journal September 2005
Conformational Transitions of Adenylate Kinase: Switching by Cracking journal March 2007
Correlation of Levels of Folded Recombinant p53 in Escherichia coli with Thermodynamic Stability in Vitro journal September 2007
Amyloid Fibril Formation by the Glaucoma-Associated Olfactomedin Domain of Myocilin journal August 2012
The Glaucoma-Associated Olfactomedin Domain of Myocilin Forms Polymorphic Fibrils That Are Constrained by Partial Unfolding and Peptide Sequence journal February 2014
Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability journal July 2016
Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability journal April 2018
Gene–environment interactions in ocular diseases journal July 2009
Stability effects of mutations and protein evolvability journal October 2009
Ensemble Refinement of Protein Crystal Structures: Validation and Application journal September 2007
Helix Cracking Regulates the Critical Interaction between RetS and GacS in Pseudomonas aeruginosa journal May 2019
Regulated unfolding: a basic principle of intraprotein signaling in modular proteins journal November 2013
Biological Roles of Protein Kinetic Stability journal November 2017
Trifunctional High-Throughput Screen Identifies Promising Scaffold To Inhibit Grp94 and Treat Myocilin-Associated Glaucoma journal February 2018
The Stability of Myocilin Olfactomedin Domain Variants Provides New Insight into Glaucoma as a Protein Misfolding Disorder journal July 2011
Rescue of Glaucoma-Causing Mutant Myocilin Thermal Stability by Chemical Chaperones journal March 2010
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles journal August 2012
Energy landscapes of functional proteins are inherently risky journal October 2014
Calcium modulates force sensing by the von Willebrand factor A2 domain journal July 2011
Missense meanderings in sequence space: a biophysical view of protein evolution journal August 2005
Mechanotransduction at a distance: mechanically coupling the extracellular matrix with the nucleus journal January 2009
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome journal December 2019
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation journal February 2021
Isoform-selective Hsp90 inhibition rescues model of hereditary open-angle glaucoma journal December 2017
Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases journal January 2021
Comparison of simple potential functions for simulating liquid water journal July 1983
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems journal June 1993
Constant pressure molecular dynamics simulation: The Langevin piston method journal September 1995
Protein stability promotes evolvability journal March 2006
CRISPR-Cas9–based treatment of myocilin-associated glaucoma journal October 2017
A relationship between protein stability and protein function. journal January 1995
Glucose-regulated Protein 94 Triage of Mutant Myocilin through Endoplasmic Reticulum-associated Degradation Subverts a More Efficient Autophagic Clearance Mechanism journal October 2012
The Glaucoma-associated Olfactomedin Domain of Myocilin Is a Novel Calcium Binding Protein journal November 2012
The Olfactomedin Domain from Gliomedin Is a β-Propeller with Unique Structural Properties journal December 2014
Secreted gliomedin is a perinodal matrix component of peripheral nerves journal May 2007
Prevalence of Mutations in TIGR/Myocilin in Patients with Adult and Juvenile Primary Open-Angle Glaucoma journal November 1998
Intraocular Pressure Homeostasis: Maintaining Balance in a High-Pressure Environment journal March 2014
A Cellular Assay Distinguishes Normal and Mutant TIGR/Myocilin Protein journal November 1999
Reversal of mutant myocilin non-secretion and cell killing: implications for glaucoma journal April 2004
Exploiting the interaction between Grp94 and aggregated myocilin to treat glaucoma journal July 2014
Structural basis for misfolding in myocilin-associated glaucoma journal December 2014
Genetics of glaucoma journal May 2017
Prevalence of Myocilin Mutations in Adults with Primary Open-angle Glaucoma in Ghana, West Africa journal January 2002
Stress Response of the Trabecular Meshwork journal January 2008
The Nodes of Ranvier: Molecular Assembly and Maintenance journal September 2015
Phaser crystallographic software journal July 2007
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Features and development of Coot journal March 2010
Towards automated crystallographic structure refinement with phenix.refine journal March 2012
Protein Dynamism and Evolvability journal April 2009
Identification of a Gene That Causes Primary Open Angle Glaucoma journal January 1997
In vivo aspects of protein folding and quality control journal June 2016
Regulation of Trabecular Meshwork Contractility journal January 2000
Intracellular Sequestration of Hetero-oligomers Formed by Wild-Type and Glaucoma-Causing Myocilin Mutants journal October 2004
Extracellular Matrix Gene Alternative Splicing by Trabecular Meshwork Cells in Response to Mechanical Stretching journal March 2007
The Cell and Molecular Biology of Glaucoma: Biomechanical Factors in Glaucoma journal May 2012
Reduction of ER stress via a chemical chaperone prevents disease phenotypes in a mouse model of primary open angle glaucoma journal September 2011
Reduction of ER stress via a chemical chaperone prevents disease phenotypes in a mouse model of primary open angle glaucoma journal August 2015
Mechanisms of protein-folding diseases at a glance journal January 2014
How Protein Stability and New Functions Trade Off journal February 2008
ECOD: An Evolutionary Classification of Protein Domains journal December 2014
Biophysical Characterization of the Olfactomedin Domain of Myocilin, an Extracellular Matrix Protein Implicated in Inherited Forms of Glaucoma journal January 2011
Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies journal June 2015
PHENIX: a comprehensive Python-based system for macromolecular structure solution. text January 2010
Olfactomedin proteins: central players in development and disease journal January 2014

Cited By (1)

Calcium-ligand variants of the myocilin olfactomedin propeller selected from invertebrate phyla reveal cross-talk with N-terminal blade and surface helices journal August 2019