scholarly journals Fast computational mutation-response scanning of proteins

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11330
Author(s):  
Julian Echave
Keyword(s):  
Protein Complexes ◽  
Point Mutations ◽  
Structural Evolution ◽  
Single Mutation ◽  
Large Protein ◽  
Sensitivity Matrix ◽  
Double Mutation ◽  
Protein Databases ◽  
Simulation Based ◽  
Protein Research

Studying the effect of perturbations on protein structure is a basic approach in protein research. Important problems, such as predicting pathological mutations and understanding patterns of structural evolution, have been addressed by computational simulations that model mutations using forces and predict the resulting deformations. In single mutation-response scanning simulations, a sensitivity matrix is obtained by averaging deformations over point mutations. In double mutation-response scanning simulations, a compensation matrix is obtained by minimizing deformations over pairs of mutations. These very useful simulation-based methods may be too slow to deal with large proteins, protein complexes, or large protein databases. To address this issue, I derived analytical closed formulas to calculate the sensitivity and compensation matrices directly, without simulations. Here, I present these derivations and show that the resulting analytical methods are much faster than their simulation counterparts.

scholarly journals Fast and exact single and double mutation-response scanning of proteins

2020 ◽  
Author(s):  
Julian Echave
Keyword(s):  
Analytical Methods ◽  
Point Mutations ◽  
Structural Evolution ◽  
Molecular Complexes ◽  
Single Mutation ◽  
Computational Simulations ◽  
Sensitivity Matrix ◽  
Double Mutation ◽  
Simulation Based ◽  
Protein Research

AbstractStudying the effect of perturbations on protein structure is a basic approach in protein research. Important problems, such as predicting pathological mutations and understanding patterns structural evolution, have been addressed by computational simulations based on modelling mutations as forces and predicting deformations using the Linear Response Approximation. In single mutation-response scanning simulations, a sensitivity matrix is obtained by averaging deformations over point mutations. In double mutation-response scanning simulations, a compensation matrix is obtained by minimizing deformations over pairs of mutations. These very useful simulation-based methods may be too slow to deal with large supra-molecular complexes, such as a ribosome or a virus capsid, or large number of proteins, such as the human proteome, which limits their applicability. To address this issue, I derived analytical closed formulas to calculate the sensitivity and compensation matrices directly, without simulations. Here, I present these derivations and show that the resulting analytical methods are much faster than their simulation counterparts, and that where the simulation methods are approximate, the analytical methods are exact by design.

scholarly journals Tafazzins from Drosophila and mammalian cells assemble in large protein complexes with a short half-life

Mitochondrion ◽  
2015 ◽  
Vol 21 ◽  
pp. 27-32 ◽  
Author(s):  
Yang Xu ◽  
Ashim Malhotra ◽  
Steven M. Claypool ◽  
Mindong Ren ◽  
Michael Schlame
Keyword(s):  
Half Life ◽  
Mammalian Cells ◽  
Protein Complexes ◽  
Large Protein ◽  
Short Half Life

Domains of the rat rDNA promoter must be aligned stereospecifically

1992 ◽  
Vol 12 (3) ◽  
pp. 1266-1275
Author(s):  
W Q Xie ◽  
L I Rothblum
Keyword(s):  
Protein Complexes ◽  
Point Mutations ◽  
In Vitro Transcription ◽  
Promoter Elements ◽  
Repeat Distance ◽  
Deletion Mutations ◽  
The Core ◽  
In Vivo Experiments

Efficient transcription from the rat rDNA promoter results from an undefined interaction between the core (CPE) and upstream (UPE) promoter elements or the protein complexes which form on them. These interactions were demonstrated by the behavior of promoters that contained either linker-scanning or deletion mutations of the UPE in combination with point mutations of the CPE (bidomain mutants). In vivo transcription experiments using point mutations within the CPE (G----A mutation at either -16 or -7) demonstrated that the CPE may in fact consist of two domains. Whereas both of these mutants were rescued by the addition of UBF to in vitro transcription reactions, the CPE mutant -7A/G was inactive in vivo. Experiments with these bidomain mutants demonstrated that the UPE was required for the rescue of the CPE mutants. We also examined the hypothesis that this interaction might require a stereospecific alignment of the promoter elements. Our results indicate that the promoter consists of several domains with differing responses to mutations that alter the distance between, or within, the promoter elements. For example, the insertion or deletion of half-multiples of the helical repeat distance between -167 and -147 had no significant effect on transcription. On the other hand, some sites were sensitive to deletions of any size but not to insertions of up to 20 bp. The analyses of two sites yielded results suggesting that they lay between domains of the promoter that must be on the same side of the DNA helix for promoter activity. The first of these sites mapped between -106 and -95.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Phenotypes of vesicular stomatitis virus mutants with mutations in the PSAP motif of the matrix protein

2012 ◽  
Vol 93 (4) ◽  
pp. 857-865 ◽  
Author(s):  
Linda Obiang ◽  
Hélène Raux ◽  
Malika Ouldali ◽  
Danielle Blondel ◽  
Yves Gaudin
Keyword(s):  
Vesicular Stomatitis Virus ◽  
Matrix Protein ◽  
Virus Assembly ◽  
Susceptibility Gene ◽  
Point Mutations ◽  
Binding Motif ◽  
Single Mutation ◽  
Amino Terminal ◽  
Vesicular Stomatitis ◽  
Late Domains

Vesicular stomatitis virus (VSV) matrix protein (M) has a flexible amino-terminal part that recruits cellular partners. It contains a dynamin-binding site that is required for efficient virus assembly, and two motifs, 24PPPY27 and 37PSAP40, that constitute potential late domains. Late domains are present in proteins of several enveloped viruses and are involved in the ultimate step of the budding process (i.e. fission between viral and cellular membranes). In baby hamster kidney (BHK)-21 cells, it has been demonstrated that the 24PPPY27 motif binds the Nedd4 (neuronal precursor cell-expressed developmentally downregulated 4) E3 ubiquitin ligase for efficient virus budding and that the 37PSAP40 motif, although conserved among M proteins of vesiculoviruses, does not possess late-domain activity. In this study, we have re-examined the contribution of the PSAP motif to VSV budding. First, we demonstrate that VSV M indeed binds TSG101 [tumour susceptibility gene 101; a component of the ESCRT1 (endosomal sorting complex required for transport 1)] through its PSAP motif. Second, we analysed the phenotype of several recombinant mutants. We show that a double mutant with point mutations in both the PSAP and the PPPY motifs is impaired compared with a single mutant in the PPPY motif, indicating that the PSAP motif partially compensates for the lack of the PPPY motif. Mutants’ phenotypes depend on cell lines: in CERA (chicken embryo-related, Alger clone) cells, a recombinant virus with a single mutation in the PSAP motif was impaired compared with the wild type, and a mutant with a single mutation in the dynamin-binding motif was much less impaired in Vero cells than in BSR (clones of BHK-21) cells. These results have implications for the VSV budding pathway that will be discussed.

scholarly journals Double Mutations in Succinate Dehydrogenase Are Involved in SDHI Resistance in Corynespora cassiicola

2022 ◽  
Vol 10 (1) ◽  
pp. 132
Author(s):  
Bingxue Sun ◽  
Guangxue Zhu ◽  
Xuewen Xie ◽  
Ali Chai ◽  
Lei Li ◽  
...  
Keyword(s):  
Succinate Dehydrogenase ◽  
Point Mutation ◽  
Single Point ◽  
Resistance Management ◽  
Site Directed Mutagenesis ◽  
Single Point Mutation ◽  
Single Mutation ◽  
Corynespora Cassiicola ◽  
Double Mutation ◽  
Mutation Analyses

With the further application of succinate dehydrogenase inhibitors (SDHI), the resistance caused by double mutations in target gene is gradually becoming a serious problem, leading to a decrease of control efficacy. It is important to assess the sensitivity and fitness of double mutations to SDHI in Corynespora cassiicola and analysis the evolution of double mutations. We confirmed, by site-directed mutagenesis, that all double mutations (B-I280V+D-D95E/D-G109V/D-H105R, B-H278R+D-D95E/D-G109V, B-H278Y+D-D95E/D-G109V) conferred resistance to all SDHI and exhibited the increased resistance to at least one fungicide than single point mutation. Analyses of fitness showed that all double mutations had lower fitness than the wild type; most of double mutations suffered more fitness penalties than the corresponding single mutants. We also further found that double mutations (B-I280V+D-D95E/D-G109V/D-H105R) containing low SDHI-resistant single point mutation (B-I280V) exhibited higher resistance to SDHI and low fitness penalty than double mutations (B-H278Y+D-D95E/D-G109V) containing high SDHI-resistant single mutations (B-H278Y). Therefore, we may infer that a single mutation conferring low resistance is more likely to evolve into a double mutation conferring higher resistance under the selective pressure of SDHI. Taken together, our results provide some important reference for resistance management.

scholarly journals The right place at the right time: Aurora B kinase localization to centromeres and kinetochores

2020 ◽  
Vol 64 (2) ◽  
pp. 299-311 ◽  
Author(s):  
Amanda J. Broad ◽  
Jennifer G. DeLuca
Keyword(s):  
Spindle Assembly Checkpoint ◽  
Protein Complexes ◽  
Centromeric Heterochromatin ◽  
Aurora B ◽  
Mitotic Chromosomes ◽  
Large Protein ◽  
Aurora B Kinase ◽  
Centromeric Protein ◽  
Spindle Microtubules ◽  
The Right

Abstract The fidelity of chromosome segregation during mitosis is intimately linked to the function of kinetochores, which are large protein complexes assembled at sites of centromeric heterochromatin on mitotic chromosomes. These key “orchestrators” of mitosis physically connect chromosomes to spindle microtubules and transduce forces through these connections to congress chromosomes and silence the spindle assembly checkpoint. Kinetochore-microtubule attachments are highly regulated to ensure that incorrect attachments are not prematurely stabilized, but instead released and corrected. The kinase activity of the centromeric protein Aurora B is required for kinetochore-microtubule destabilization during mitosis, but how the kinase acts on outer kinetochore substrates to selectively destabilize immature and erroneous attachments remains debated. Here, we review recent literature that sheds light on how Aurora B kinase is recruited to both centromeres and kinetochores and discuss possible mechanisms for how kinase interactions with substrates at distinct regions of mitotic chromosomes are regulated.

scholarly journals Molecular requirements for the formation of a kinetochore–microtubule interface by Dam1 and Ndc80 complexes

2012 ◽  
Vol 200 (1) ◽  
pp. 21-30 ◽  
Author(s):  
Fabienne Lampert ◽  
Christine Mieck ◽  
Gregory M. Alushin ◽  
Eva Nogales ◽  
Stefan Westermann
Keyword(s):  
Chromosome Segregation ◽  
Protein Complexes ◽  
Structural Elements ◽  
Large Protein ◽  
Kinetochore Assembly ◽  
Sister Chromatids ◽  
Dam1 Complex ◽  
Shed Light ◽  
Kinetochore Function

Kinetochores are large protein complexes that link sister chromatids to the spindle and transduce microtubule dynamics into chromosome movement. In budding yeast, the kinetochore–microtubule interface is formed by the plus end–associated Dam1 complex and the kinetochore-resident Ndc80 complex, but how they work in combination and whether a physical association between them is critical for chromosome segregation is poorly understood. Here, we define structural elements required for the Ndc80–Dam1 interaction and probe their function in vivo. A novel ndc80 allele, selectively impaired in Dam1 binding, displayed growth and chromosome segregation defects. Its combination with an N-terminal truncation resulted in lethality, demonstrating essential but partially redundant roles for the Ndc80 N-tail and Ndc80–Dam1 interface. In contrast, mutations in the calponin homology domain of Ndc80 abrogated kinetochore function and were not compensated by the presence of Dam1. Our experiments shed light on how microtubule couplers cooperate and impose important constraints on structural models for outer kinetochore assembly.

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