One sequence plus one mutation equals two folds

Shortle, David

doi:10.1073/pnas.0912370107

Cited by 13 publications

(16 citation statements)

References 12 publications

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“…Summarily, the bending of N and C termini and the III 88 conformation with the 5 full unfolded segments also are crucial factors in the structural transition from the 3α fold form of GA88-M to the α+4β fold form of GB88. This result also supports the experimental suggestion for the critical role of N and C termini in this switch 24,29. To explore the allosteric communications of each residue along this transition pathway of the GA88-M to GB88 states, we constructed and analyzed the motion correlations for all Cα atoms of GA88-M to GB88 from the simulation trajectories.…”

supporting

confidence: 78%

Section: Resultsmentioning

confidence: 99%

“…For example, in the hypothesis reported by Fabio Polticelli, the conversion from G A to G B could help bacteria to efficiently extract fatty acids. It has been confirmed that the N and C termini in the conversion of G A to G B play a critical role in fold switching with hydrophobic core converting . The studies on the presence of an intermediate with reduced native contacts during the unfolding process from G B state to its unfolded state, and further investigations of the similar folding directions for G A 88 or G B 88 state have been performed by Gianni, Samuel, and co‐workers using equilibrium and kinetic folding/unfolding experiments, and molecular dynamics (MD) simulations .…”

Section: Introductionmentioning

confidence: 98%

“…It has been confirmed that the N and C termini in the conversion of G A to G B play a critical role in fold switching with hydrophobic core converting. 24,29 The studies on the presence of an intermediate with reduced native contacts during the unfolding process from G B state to its unfolded state, and further investigations of the similar folding directions for G A 88 or G B 88 state have been performed by Gianni, Samuel, and coworkers using equilibrium and kinetic folding/unfolding experiments, and molecular dynamics (MD) simulations. [30][31][32][33][34] The folding mechanisms and stability for the G A 98, G B 98 states and their mutants were investigated using the free energy surface calculations and the allatom/coarse-grained models.…”

Section: Introductionmentioning

confidence: 99%

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Molecular dynamics simulations on the conformational transitions from the G_A98 (G_A88) to G_B98 (G_B88) proteins

Song

Wang

Xue

et al. 2016

J of Molecular Recognition

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We performed conventional and targeted molecular dynamics simulations to address the dynamic transition mechanisms of the conformational transitions from the G 98 protein with only 1 mutation of Leu45Tyr to G 98 and from the G 88 protein with 7 mutations of Gly24Ala, Ile25Thr, Ile30Phe, Ile33Tyr, Leu45Tyr, Ile49Thr, and Leu50Lys to G 88. The results show that the conformational transition mechanism from the mutated 3α G 98 (G 88) state to the α+4β G 98 (G 88) state via several intermediate conformations involves the bending of loops at the N and C termini firstly, the unfolding of αA and αC, then the traversing of αB, and the formation of the 4β layer with the conversion of the hydrophobic core. The bending of loops at the N and C termini and the formation of the crucial transition conformation with the full unfolded structure are key factors in their transition processes. The communication of the interaction network, the bending directions of loops, and the traversing site of αB in the transition of G 98 to G 98 are markedly different from those in G 88 to G 88 because of the different mutated residues. The analysis of the correlations and the calculated mass center distances between some segments further supported their conformational transition mechanisms. These results could help people to better understand the Paracelsus challenge. Copyright © 2016 John Wiley & Sons, Ltd.

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supporting

confidence: 78%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

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Molecular dynamics simulations on the conformational transitions from the G_A98 (G_A88) to G_B98 (G_B88) proteins

Song

Wang

Xue

et al. 2016

J of Molecular Recognition

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“…The reported change is dramatic. One structure is a three-helix bundle, and the other has a four-stranded β-sheet with a single α-helix; 85% of the residues change their secondary structure, with only eight residues in the central α-helix plus one or two turn residues retaining the same conformation in both structures (111).…”

Section: Conformational Changes Not Due To Environmentmentioning

confidence: 99%

On the Universe of Protein Folds

Kolodny

Pereyaslavets

Samson

et al. 2013

Annu. Rev. Biophys.

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In the fifty years since the first atomic structure of a protein was revealed, tens of thousands of additional structures have been solved. Like all objects in biology, proteins structures show common patterns that seem to define family relationships. Classification of proteins structures, which started in the 1970s with about a dozen structures, has continued with increasing enthusiasm, leading to two main fold classifications, SCOP and CATH, as well as many additional databases. Classification is complicated by deciding what constitutes a domain, the fundamental unit of structure. Also difficult is deciding when two given structures are similar. Like all of biology, fold classification is beset by exceptions to all rules. Thus, the perspectives of protein fold space that the fold classifications offer differ from each other. In spite of these ambiguities, fold classifications are useful for prediction of structure and function. Studying the characteristics of fold space can shed light on protein evolution and the physical laws that govern protein behavior.

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Mechanisms of protein evolution

et al. 2022

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How do proteins evolve? How do changes in sequence mediate changes in protein structure, and in turn in function? This question has multiple angles, ranging from biochemistry and biophysics to evolutionary biology. This review provides a brief integrated view of some key mechanistic aspects of protein evolution. First, we explain how protein evolution is primarily driven by randomly acquired genetic mutations and selection for function, and how these mutations can even give rise to completely new folds. Then, we also comment on how phenotypic protein variability, including promiscuity, transcriptional and translational errors, may also accelerate this process, possibly via "plasticity-first" mechanisms. Finally, we highlight open questions in the field of protein evolution, with respect to the emergence of more sophisticated protein systems such as protein complexes, pathways, and the emergence of pre-LUCA enzymes.

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One sequence plus one mutation equals two folds

Cited by 13 publications

References 12 publications

Molecular dynamics simulations on the conformational transitions from the G_A98 (G_A88) to G_B98 (G_B88) proteins

Molecular dynamics simulations on the conformational transitions from the G_A98 (G_A88) to G_B98 (G_B88) proteins

On the Universe of Protein Folds

Mechanisms of protein evolution

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One sequence plus one mutation equals two folds

Cited by 13 publications

References 12 publications

Molecular dynamics simulations on the conformational transitions from the GA98 (GA88) to GB98 (GB88) proteins

Molecular dynamics simulations on the conformational transitions from the GA98 (GA88) to GB98 (GB88) proteins

On the Universe of Protein Folds

Mechanisms of protein evolution

Contact Info

Product

Resources

About

Molecular dynamics simulations on the conformational transitions from the G_A98 (G_A88) to G_B98 (G_B88) proteins

Molecular dynamics simulations on the conformational transitions from the G_A98 (G_A88) to G_B98 (G_B88) proteins