Correlated mutation analyses on super-family alignments reveal functionally important residues

2009 ◽  
Vol 76 (3) ◽  
pp. 608-616 ◽  
Author(s):  
Remko K. P. Kuipers ◽  
Henk-Jan Joosten ◽  
Eugene Verwiel ◽  
Sjoerd Paans ◽  
Jasper Akerboom ◽  
...  
Keyword(s):  
Correlated Mutation ◽  
Mutation Analyses

Correlated Mutation Analyses on Very Large Sequence Families

ChemBioChem ◽  
2002 ◽  
Vol 3 (10) ◽  
pp. 1010-1017 ◽  
Author(s):  
L. Oliveira ◽  
A. C. M. Paiva ◽  
G. Vriend
Keyword(s):  
Correlated Mutation ◽  
Mutation Analyses

scholarly journals Structure and mechanism of the ATP synthase membrane motor inferred from quantitative integrative modeling

2016 ◽  
Vol 148 (6) ◽  
pp. 441-457 ◽  
Author(s):  
Vanessa Leone ◽  
José D. Faraldo-Gómez
Keyword(s):  
Atp Synthase ◽  
Binding Sites ◽  
Transmembrane Domain ◽  
Structural Information ◽  
Integrative Approach ◽  
Subunit A ◽  
C Complex ◽  
Biochemical Analyses ◽  
Correlated Mutation ◽  
Mutation Analyses

Two subunits within the transmembrane domain of the ATP synthase—the c-ring and subunit a—energize the production of 90% of cellular ATP by transducing an electrochemical gradient of H+ or Na+ into rotational motion. The nature of this turbine-like energy conversion mechanism has been elusive for decades, owing to the lack of definitive structural information on subunit a or its c-ring interface. In a recent breakthrough, several structures of this complex were resolved by cryo–electron microscopy (cryo-EM), but the modest resolution of the data has led to divergent interpretations. Moreover, the unexpected architecture of the complex has cast doubts on a wealth of earlier biochemical analyses conducted to probe this structure. Here, we use quantitative molecular-modeling methods to derive a structure of the a–c complex that is not only objectively consistent with the cryo-EM data, but also with correlated mutation analyses of both subunits and with prior cross-linking and cysteine accessibility measurements. This systematic, integrative approach reveals unambiguously the topology of subunit a and its relationship with the c-ring. Mapping of known Cd2+ block sites and conserved protonatable residues onto the structure delineates two noncontiguous pathways across the complex, connecting two adjacent proton-binding sites in the c-ring to the space on either side of the membrane. The location of these binding sites and of a strictly conserved arginine on subunit a, which serves to prevent protons from hopping between them, explains the directionality of the rotary mechanism and its strict coupling to the proton-motive force. Additionally, mapping of mutations conferring resistance to oligomycin unexpectedly reveals that this prototypical inhibitor may bind to two distinct sites at the a–c interface, explaining its ability to block the mechanism of the enzyme irrespective of the direction of rotation of the c-ring. In summary, this study is a stepping stone toward establishing the mechanism of the ATP synthase at the atomic level.

scholarly journals Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcus furiosus Phosphoglucose Isomerase

Biomolecules ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 212 ◽  
Author(s):  
Kalyanasundaram Subramanian ◽  
Karolina Mitusińska ◽  
John Raedts ◽  
Feras Almourfi ◽  
Henk-Jan Joosten ◽  
...  
Keyword(s):  
Protein Engineering ◽  
Specific Activity ◽  
Pyrococcus Furiosus ◽  
Phosphoglucose Isomerase ◽  
Biochemical Activity ◽  
Metal Cofactor ◽  
Access Regulation ◽  
Functional Relevance ◽  
Correlated Mutation ◽  
Mutation Analyses

The cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic archaeon Pyrococcus furiosus catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. We investigated PfPGI using protein-engineering bioinformatics tools to select functionally-important residues based on correlated mutation analyses. A pair of amino acids in the periphery of PfPGI was found to be the dominant co-evolving mutation. The position of these selected residues was found to be non-obvious to conventional protein engineering methods. We designed a small smart library of variants by substituting the co-evolved pair and screened their biochemical activity, which revealed their functional relevance. Four mutants were further selected from the library for purification, measurement of their specific activity, crystal structure determination, and metal cofactor coordination analysis. Though the mutant structures and metal cofactor coordination were strikingly similar, variations in their activity correlated with their fine-tuned dynamics and solvent access regulation. Alternative, small smart libraries for enzyme optimization are suggested by our approach, which is able to identify non-obvious yet beneficial mutations.

scholarly journals Mutation analyses in pedigrees and sporadic cases of ethnic Han Chinese Kallmann syndrome patients

2015 ◽  
Vol 240 (11) ◽  
pp. 1480-1489 ◽  
Author(s):  
Wei-Jun Gu ◽  
Qian Zhang ◽  
Ying-Qian Wang ◽  
Guo-Qing Yang ◽  
Tian-Pei Hong ◽  
...  
Keyword(s):  
Kallmann Syndrome ◽  
Han Chinese ◽  
Sporadic Cases ◽  
Mutation Analyses

Mutation Analyses of PROP1 in 24 Patients with Combined Pituitary Hormone Deficiency: Identification of a Novel Substitution

2011 ◽  
pp. P1-266-P1-266
Author(s):  
Debora Cristina Moraes ◽  
Karina Schiavoni Scandelai Cardoso dos Reis ◽  
Gisele Dazzi Lorenzoni ◽  
Flavia Lucia Conceicao ◽  
Mario Vaismann ◽  
...  
Keyword(s):  
Hormone Deficiency ◽  
Pituitary Hormone ◽  
Pituitary Hormone Deficiency ◽  
Combined Pituitary Hormone Deficiency ◽  
Mutation Analyses

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.

Optimal data collection for correlated mutation analysis

2009 ◽  
Vol 74 (3) ◽  
pp. 545-555 ◽  
Author(s):  
Haim Ashkenazy ◽  
Ron Unger ◽  
Yossef Kliger
Keyword(s):  
Data Collection ◽  
Mutation Analysis ◽  
Correlated Mutation
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