Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle.


Abstract

Self-assembling proteins are critical to biological systems and industrial technologies, but predicting how mutations affect self-assembly remains a significant challenge. Here, we report a technique, termed SyMAPS (Systematic Mutation and Assembled Particle Selection), that can be used to characterize the assembly competency of all single amino acid variants of a self-assembling viral structural protein. SyMAPS studies on the MS2 bacteriophage coat protein revealed a high-resolution fitness landscape that challenges some conventional assumptions of protein engineering. An additional round of selection identified a previously unknown variant (CP[T71H]) that is stable at neutral pH but less tolerant to acidic conditions than the wild-type coat protein. The capsids formed by this variant could be more amenable to disassembly in late endosomes or early lysosomes-a feature that is advantageous for delivery applications. In addition to providing a mutability blueprint for virus-like particles, SyMAPS can be readily applied to other self-assembling proteins.

Submission Details

ID: 2VxwaJVT

Submitter: Shu-Ching Ou

Submission Date: Dec. 20, 2018, 4:51 p.m.

Version: 1

Publication Details
Hartman EC;Jakobson CM;Favor AH;Lobba MJ;Álvarez-Benedicto E;Francis MB;Tullman-Ercek D,Nat Commun (2018) Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle. PMID:29643335
Additional Information

Study Summary

Number of data points 2452
Proteins Capsid protein
Unique complexes 2452
Assays/Quantities/Protocols Experimental Assay: Apparent Fitness Scores
Libraries Variants for Capsid Protein

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1AQ3 1997-08-06T00:00:00+0000 2.8 BACTERIOPHAGE MS2 CAPSID PROTEIN/RNA COMPLEX
1AQ4 1997-08-06T00:00:00+0000 3.0 STRUCTURE OF A MS2 COAT PROTEIN MUTANT IN COMPLEX WITH AN RNA OPERATOR
1BMS 1995-08-29T00:00:00+0000 2.7 CRYSTAL STRUCTURE OF MS2 CAPSIDS WITH MUTATIONS IN THE SUBUNIT FG LOOP
1MSC 1995-04-28T00:00:00+0000 2.0 CRYSTAL STRUCTURE OF MS2 COAT PROTEIN DIMER
1MST 1995-08-30T00:00:00+0000 2.6 CRYSTAL STRUCTURE OF MS2 CAPSIDS WITH MUTATIONS IN THE SUBUNIT FG LOOP
1MVA 1997-08-06T00:00:00+0000 3.0 STRUCTURE OF A PROTEIN CAPSID OF THE T45A MUTANT OF PHAGE MS2
1MVB 1997-08-06T00:00:00+0000 3.0 STRUCTURE OF A PROTEIN CAPSID OF THE T59S MUTANT OF PHAGE MS2
1U1Y 2004-07-16T00:00:00+0000 2.85 Crystal structure of a complex between WT bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position
1ZDH 1996-09-24T00:00:00+0000 2.7 MS2 COAT PROTEIN/RNA COMPLEX
1ZDI 1996-09-24T00:00:00+0000 2.7 RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
290.70000000000005 A,B,C Capsid protein P03611 CAPSD_BPF2
293.1 A,B,C Capsid protein P69171 CAPSD_BPZR
293.1 A,B,C Capsid protein P69170 CAPSD_BPR17
300.0 A,B,C Capsid protein P03612 CAPSD_BPMS2