scholarly journals Beyond Rotatable Bond Counts: Capturing 3D Conformational Flexibility in a Single Descriptor

2016 ◽  
Vol 56 (12) ◽  
pp. 2347-2352 ◽  
Author(s):  
Jerome G. P. Wicker ◽  
Richard I. Cooper
Keyword(s):  
Conformational Flexibility ◽  
Rotatable Bond

The model rotator phase

1988 ◽  
Vol 53 (5) ◽  
pp. 889-902
Author(s):  
Josef Šebek
Keyword(s):  
High Temperature ◽  
Partition Function ◽  
Conformational Flexibility ◽  
Small Probability ◽  
Crystalline Phases ◽  
Rotator Phase

It is shown that the formation of the so-called rotator phase of alkanes (one of the high temperature crystalline phases) might be connected with a partial increase of the conformational flexibility of chains. The conformations with higher number of kinks per chain, which have been neglected till now, are shown to contribute effectively to the conformational partition function. Small probability of these states given by the Boltzmann exponent is compensated by a large number of ways in which they can be distributed along the chain. The deduced features of the rotator phase seem to be in agreement with the experimentally observed properties.

scholarly journals Solid-State Conformational Flexibility at Work: Energetic Landscape of a Single Crystal-to-Single Crystal Transformation in a Cyclic Hexapeptoid

2021 ◽  
Vol 21 (2) ◽  
pp. 897-907
Author(s):  
Giovanni Pierri ◽  
Marta Corno ◽  
Eleonora Macedi ◽  
Maria Voccia ◽  
Consiglia Tedesco
Keyword(s):  
Solid State ◽  
Single Crystal ◽  
Conformational Flexibility ◽  
Crystal Transformation

scholarly journals Analysis of Sequence Divergence in Mammalian ABCGs Predicts a Structural Network of Residues That Underlies Functional Divergence

2021 ◽  
Vol 22 (6) ◽  
pp. 3012
Author(s):  
James I. Mitchell-White ◽  
Thomas Stockner ◽  
Nicholas Holliday ◽  
Stephen J. Briddon ◽  
Ian D. Kerr
Keyword(s):  
Substrate Specificity ◽  
Functional Divergence ◽  
3D Structure ◽  
Sequence Divergence ◽  
Conformational Flexibility ◽  
Substrate Selectivity ◽  
Multiple Sequence ◽  
Atp Binding Cassette Transporters ◽  
Structural Network ◽  
Wide Substrate Specificity

The five members of the mammalian G subfamily of ATP-binding cassette transporters differ greatly in their substrate specificity. Four members of the subfamily are important in lipid transport and the wide substrate specificity of one of the members, ABCG2, is of significance due to its role in multidrug resistance. To explore the origin of substrate selectivity in members 1, 2, 4, 5 and 8 of this subfamily, we have analysed the differences in conservation between members in a multiple sequence alignment of ABCG sequences from mammals. Mapping sets of residues with similar patterns of conservation onto the resolved 3D structure of ABCG2 reveals possible explanations for differences in function, via a connected network of residues from the cytoplasmic to transmembrane domains. In ABCG2, this network of residues may confer extra conformational flexibility, enabling it to transport a wider array of substrates.

scholarly journals Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Gloria Gamiz-Arco ◽  
Luis I. Gutierrez-Rus ◽  
Valeria A. Risso ◽  
Beatriz Ibarra-Molero ◽  
Yosuke Hoshino ◽  
...  
Keyword(s):  
Sequence Space ◽  
Conformational Flexibility ◽  
Allosteric Modulation ◽  
Heme Binding ◽  
Optimum Temperature ◽  
Glycosidic Bonds ◽  
Glycosidase Activity ◽  
Tim Barrel ◽  
Crystallographic Structures ◽  
Ancestral Protein

AbstractGlycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.

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