Visualizing Deep Mutational Scan Data

AbstractSite-directed and random mutagenesis are biochemical tools to obtain insights into the structure and function of proteins. Recent advances such as deep mutational scan have allowed a complete scan of all the amino acid positions in a protein with each of the 19 possible alternatives. Mapping out the phenotypic consequences of thousands of single point mutations in the same protein is now possible. Visualizing and analysing the rich data offers an opportunity to learn more about the effects of mutations, for a better understanding and engineering of proteins. This work focuses on such visualization analyses applied to the mutational data of TEM-1 β-lactamase. The data is examined in the light of the expected biochemical effects of single point mutations, with the goal of reinforcing or retraining the intuitions. Individual attributes of the amino acid mutations such as the solvent accessible area, charge type change, and distance from the catalytic center capture most of the relevant functional effects. Visualizing the data suggests how combinations of these attributes can be used for a better classification of the effects of mutations, when independently they do not offer a high predictability.

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Single point mutations reveal amino acid residues important for Chromobacterium violaceum transaminase activity in the production of unnatural amino acids

Scientific Reports ◽

10.1038/s41598-018-35688-7 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 3

Author(s):

Sarah A. Almahboub ◽

Tanja Narancic ◽

Darren Fayne ◽

Kevin E. O’Connor

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Unnatural Amino Acids ◽

Single Point ◽

Point Mutations ◽

Chromobacterium Violaceum ◽

Amino Acid Residues ◽

Transaminase Activity ◽

Single Point Mutations

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Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations

Biomolecules ◽

10.3390/biom9100611 ◽

2019 ◽

Vol 9 (10) ◽

pp. 611 ◽

Cited By ~ 2

Author(s):

Ortega ◽

Vilhena ◽

Zotti ◽

Díez-Pérez ◽

Cuevas ◽

...

Keyword(s):

Amino Acid ◽

Single Molecule ◽

Single Point ◽

Point Mutations ◽

Point Of View ◽

Single Amino Acid ◽

Theoretical Point ◽

Blue Copper ◽

Structure And Dynamics ◽

Amino Acid Mutations

In the growing field of biomolecular electronics, blue-copper Azurin stands out as one of the most widely studied protein in single-molecule contacts. Interestingly, despite the paramount importance of the structure/dynamics of molecular contacts in their transport properties, these factors remain largely unexplored from the theoretical point of view in the context of single Azurin junctions. Here we address this issue using all-atom Molecular Dynamics (MD) of Pseudomonas Aeruginosa Azurin adsorbed to a Au(111) substrate. In particular, we focus on the structure and dynamics of the free/adsorbed protein and how these properties are altered upon single-point mutations. The results revealed that wild-type Azurin adsorbs on Au(111) along two well defined configurations: one tethered via cysteine groups and the other via the hydrophobic pocket surrounding the Cu 2 + . Surprisingly, our simulations revealed that single amino-acid mutations gave rise to a quenching of protein vibrations ultimately resulting in its overall stiffening. Given the role of amino-acid vibrations and reorientation in the dehydration process at the protein-water-substrate interface, we suggest that this might have an effect on the adsorption process of the mutant, giving rise to new adsorption configurations.

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Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability—Large-Scale Validation of MD-Based Relative Free Energy Calculations

Journal of Molecular Biology ◽

10.1016/j.jmb.2016.12.007 ◽

2017 ◽

Vol 429 (7) ◽

pp. 948-963 ◽

Cited By ~ 42

Author(s):

Thomas Steinbrecher ◽

Chongkai Zhu ◽

Lingle Wang ◽

Robert Abel ◽

Christopher Negron ◽

...

Keyword(s):

Free Energy ◽

Amino Acid ◽

Protein Stability ◽

Large Scale ◽

Scale Validation ◽

Single Point ◽

Point Mutations ◽

Free Energy Calculations ◽

Relative Free Energy ◽

Single Point Mutations

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Cupin Variants as Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes

10.26434/chemrxiv.11481834.v1 ◽

2019 ◽

Author(s):

Nobutaka Fujieda ◽

Miho Yuasa ◽

Yosuke Nishikawa ◽

Genji Kurisu ◽

Shinobu Itoh ◽

...

Keyword(s):

Michael Addition ◽

In Silico ◽

Addition Reaction ◽

Single Point ◽

Point Mutations ◽

Unsaturated Ketone ◽

Michael Addition Reaction ◽

Beta Barrel ◽

Cupin Superfamily ◽

Single Point Mutations

Cupin superfamily proteins (TM1459) work as a macromolecular ligand framework with a double-stranded beta-barrel structure ligating to a Cu ion through histidine side chains. Variegating the first coordination sphere of TM1459 revealed that H52A and H54A/H58A mutants effectively catalyzed the diastereo- and enantio-selective Michael addition reaction of nitroalkanes to an α,β-unsaturated ketone. Moreover, in silico substrate docking signified C106N and F104W single-point mutations, which inverted the diastereoselectivity of H52A and further improved the stereoselectivity of H54A/H58A, respectively.

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Single-Point Mutations in Qβ Virus-like Particles Change Binding to Cells

Biomacromolecules ◽

10.1021/acs.biomac.1c00443 ◽

2021 ◽

Author(s):

Marisa L. Martino ◽

Stephen N. Crooke ◽

Marianne Manchester ◽

M.G. Finn

Keyword(s):

Single Point ◽

Point Mutations ◽

Virus Like Particles ◽

Single Point Mutations

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MinD directly interacting with FtsZ at the H10 helix suggests a model for robust activation of MinC to destabilize FtsZ polymers

Biochemical Journal ◽

10.1042/bcj20170357 ◽

2017 ◽

Vol 474 (18) ◽

pp. 3189-3205 ◽

Cited By ~ 6

Author(s):

Ashoka Chary Taviti ◽

Tushar Kant Beuria

Keyword(s):

Cell Division ◽

Single Point ◽

Point Mutations ◽

Direct Interaction ◽

Ring Formation ◽

Z Ring ◽

Single Point Mutations ◽

Biochemical Analyses ◽

Ftsz Assembly ◽

The Mind

Cell division in bacteria is a highly controlled and regulated process. FtsZ, a bacterial cytoskeletal protein, forms a ring-like structure known as the Z-ring and recruits more than a dozen other cell division proteins. The Min system oscillates between the poles and inhibits the Z-ring formation at the poles by perturbing FtsZ assembly. This leads to an increase in the FtsZ concentration at the mid-cell and helps in Z-ring positioning. MinC, the effector protein, interferes with Z-ring formation through two different mechanisms mediated by its two domains with the help of MinD. However, the mechanism by which MinD triggers MinC activity is not yet known. We showed that MinD directly interacts with FtsZ with an affinity stronger than the reported MinC–FtsZ interaction. We determined the MinD-binding site of FtsZ using computational, mutational and biochemical analyses. Our study showed that MinD binds to the H10 helix of FtsZ. Single-point mutations at the charged residues in the H10 helix resulted in a decrease in the FtsZ affinity towards MinD. Based on our findings, we propose a novel model for MinCD–FtsZ interaction, where MinD through its direct interaction with FtsZ would trigger MinC activity to inhibit FtsZ functions.

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