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
1MSC 1995-07-10 2.0 CRYSTAL STRUCTURE OF MS2 COAT PROTEIN DIMER
4ZOR 2016-09-07 2.2 The structure of the S37P MS2 viral capsid assembly.
2BU1 2005-08-18 2.2 MS2-RNA HAIRPIN (5BRU -5) COMPLEX
2C4Q 2005-11-07 2.38 MS2-RNA HAIRPIN (2ONE -5) COMPLEX
2BS0 2006-03-22 2.45 MS2 (N87AE89K mutant) - Variant Qbeta RNA hairpin complex
2IZN 2006-07-27 2.56 MS2-RNA HAIRPIN (G-10) COMPLEX
1MST 1996-03-08 2.6 CRYSTAL STRUCTURE OF MS2 CAPSIDS WITH MUTATIONS IN THE SUBUNIT FG LOOP
2C4Z 2006-01-05 2.6 MS2-RNA HAIRPIN (2SU -5-6) COMPLEX
2C50 2006-01-05 2.65 MS2-RNA HAIRPIN (A -5) COMPLEX
2C4Y 2006-01-05 2.68 MS2-RNA HAIRPIN (2THIOURACIL-5) COMPLEX
1ZDH 1997-04-21 2.7 MS2 COAT PROTEIN/RNA COMPLEX
2IZM 2007-07-03 2.7 MS2-RNA HAIRPIN (C-10) COMPLEX
1BMS 1996-03-08 2.7 CRYSTAL STRUCTURE OF MS2 CAPSIDS WITH MUTATIONS IN THE SUBUNIT FG LOOP
1ZDI 1997-04-21 2.7 RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX
1AQ3 1997-12-24 2.8 BACTERIOPHAGE MS2 CAPSID PROTEIN/RNA COMPLEX
7MSF 1998-11-11 2.8 MS2 PROTEIN CAPSID/RNA COMPLEX
2BS1 2006-03-22 2.8 MS2 (N87AE89K mutant) - Qbeta RNA hairpin complex
6MSF 1998-07-08 2.8 F6 APTAMER MS2 COAT PROTEIN COMPLEX
5MSF 1998-11-11 2.8 MS2 PROTEIN CAPSID/RNA COMPLEX
2C51 2006-01-05 2.8 MS2-RNA HAIRPIN (G -5) COMPLEX
2MS2 1995-01-26 2.8 THE REFINED STRUCTURE OF BACTERIOPHAGE MS2 AT 2.8 ANGSTROMS RESOLUTION
1U1Y 2004-12-07 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
2IZ9 2006-07-27 2.85 MS2-RNA HAIRPIN (4ONE -5) COMPLEX
1ZDK 1998-12-07 2.86 STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX
2B2D 2006-05-09 2.9 RNA stemloop operator from bacteriophage QBETA complexed with an N87S,E89K mutant MS2 capsid
1ZDJ 1998-07-08 2.9 STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX
2BQ5 2006-03-22 2.91 MS2 (N87AE89K mutant) - RNA hairpin complex
1MVA 1997-12-24 3.0 STRUCTURE OF A PROTEIN CAPSID OF THE T45A MUTANT OF PHAGE MS2
1MVB 1997-12-24 3.0 STRUCTURE OF A PROTEIN CAPSID OF THE T59S MUTANT OF PHAGE MS2
2BNY 2006-03-22 3.0 MS2 (N87A mutant) - RNA hairpin complex
1ZSE 2006-05-09 3.0 RNA stemloop from bacteriophage Qbeta complexed with an N87S mutant MS2 Capsid
1AQ4 1997-12-24 3.0 STRUCTURE OF A MS2 COAT PROTEIN MUTANT IN COMPLEX WITH AN RNA OPERATOR
2B2G 2006-05-09 3.02 MS2 Wild-type RNA stemloop complexed with an N87S mutant MS2 capsid
2B2E 2006-05-09 3.15 RNA stemloop from bacteriophage MS2 complexed with an N87S,E89K mutant MS2 capsid
2IZ8 2006-07-27 3.3 MS2-RNA HAIRPIN (C-7) COMPLEX
2VTU 2008-08-12 3.5 crystal structure of bacteriophage MS2 covalent coat protein dimer
5TC1 2016-12-07 3.6 In situ structures of the genome and genome-delivery apparatus in ssRNA bacteriophage MS2
4BP7 2013-07-17 39.0 Asymmetric structure of a virus-receptor complex
2WBH 2009-11-24 4.7 Icosahedral particle of covalent coat protein dimer of bacteriophage MS2

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