Conformational Analysis of CmH2m+1OCH2CH2OH (m = 1-4): The Role of CH.cntdot..cntdot..cntdot.O Intramolecular Interactions

A 1 TS J F,H(O) coupling pathway, dictated by a hydrogen bond, in some 2-fluorobenzoic acids has been observed, while such an interaction does not occur in 2-fluorophenol. Thus, this work reports the conformational analysis of 2-fluorophenylboronic acid (1), in order to evaluate a possible intramolecular OH∙∙∙F hydrogen bond in comparison to an nF→pB interaction, which mimics the quantum nF→σ*OH hydrogen bond that would be expected in 2-fluorophenol. 2-Fluorophenylborane (3), which does not experience hydrogen bonding, was used to verify whether nF→pB interaction governs the conformational equilibrium in 1 due to a predominant OH∙∙∙F hydrogen bond or to other effects. A series of 2-X-phenylboranes (X = Cl, Br, NH2, PH2, OH and SH) were further computationally analyzed to search for electron donors to boron, capable of influencing the conformational equilibrium. Overall, the intramolecular OH∙∙∙F hydrogen bond in 1 is quite stabilizing and dictates the 1 h J F,H(O) coupling constant. Moreover, electron donation to the empty p orbital of boron (for noncoplanar BH2 moiety relative to the phenyl ring) is also significantly stabilizing for the NH2 and PH2 derivatives, but not enough to make the corresponding conformers appreciably populated, because of steric effects and the loss of πCC→pB resonance. Thus, the results found earlier for 2-fluorophenol about the lack of intramolecular hydrogen bonding are now corroborated.

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Conformational Analysis and Intramolecular Interactions of l-Proline Methyl Ester and Its N-Acetylated Derivative through Spectroscopic and Theoretical Studies

The Journal of Physical Chemistry A ◽

10.1021/jp5007632 ◽

2014 ◽

Vol 118 (9) ◽

pp. 1748-1758 ◽

Cited By ~ 15

Author(s):

Carolyne B. Braga ◽

Lucas C. Ducati ◽

Cláudio F. Tormena ◽

Roberto Rittner

Keyword(s):

Methyl Ester ◽

Conformational Analysis ◽

Intramolecular Interactions ◽

Theoretical Studies

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Progressive Phosphorylation Modulates the Self-Association of a Variably Modified Histone H3 Peptide

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.698182 ◽

2021 ◽

Vol 8 ◽

Author(s):

George V. Papamokos ◽

George Tziatzos ◽

Dimitrios G. Papageorgiou ◽

Spyros Georgatos ◽

Efthimios Kaxiras ◽

...

Keyword(s):

Intrinsically Disordered Proteins ◽

Histone H3 ◽

Intramolecular Interactions ◽

Disordered Proteins ◽

Post Translational Modifications ◽

Intrinsically Disordered ◽

Self Association ◽

Dynamics Simulations ◽

Peptide Charge

Protein phosphorylation is a key regulatory mechanism in eukaryotic cells. In the intrinsically disordered histone tails, phosphorylation is often a part of combinatorial post-translational modifications and an integral part of the “histone code” that regulates gene expression. Here, we study the association between two histone H3 tail peptides modified to different degrees, using fully atomistic molecular dynamics simulations. Assuming that the initial conformations are either α-helical or fully extended, we compare the propensity of the two peptides to associate with one another when both are unmodified, one modified and the other unmodified, or both modified. The simulations lead to the identification of distinct inter- and intramolecular interactions in the peptide dimer, highlighting a prominent role of a fine-tuned phosphorylation rheostat in peptide association. Progressive phosphorylation appears to modulate peptide charge, inducing strong and specific intermolecular interactions between the monomers, which do not result in the formation of amorphous or ordered aggregates, as documented by experimental evidence derived from Circular Dichroism and NMR spectroscopy. However, upon complete saturation of positive charges by phosphate groups, this effect is reversed: intramolecular interactions prevail and dimerization of zero-charge peptides is markedly reduced. These findings underscore the role of phosphorylation thresholds in the dynamics of intrinsically disordered proteins. Phosphorylation rheostats might account for the divergent effects of histone modifications on the modulation of chromatin structure.

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The projection domain of MAP2b regulates microtubule protrusion and process formation in Sf9 cells

Journal of Cell Science ◽

10.1242/jcs.115.7.1523 ◽

2002 ◽

Vol 115 (7) ◽

pp. 1523-1539 ◽

Cited By ~ 1

Author(s):

Dave Bélanger ◽

Carole Abi Farah ◽

Minh Dang Nguyen ◽

Michel Lauzon ◽

Sylvie Cornibert ◽

...

Keyword(s):

Cell Surface ◽

Binding Domain ◽

Intramolecular Interactions ◽

Microtubule Assembly ◽

Sf9 Cells ◽

Microtubule Binding ◽

Process Formation ◽

Microtubule Binding Domain ◽

Projection Domain

The expression of microtubule-associated protein 2 (MAP2), developmentally regulated by alternative splicing, coincides with neurite outgrowth. MAP2 proteins contain a microtubule-binding domain (C-terminal) that promotes microtubule assembly and a poorly characterized domain, the projection domain(N-terminal), extending at the surface of microtubules. MAP2b differs from MAP2c by an additional sequence of 1372 amino acids in the projection domain. In this study, we examined the role of the projection domain in the protrusion of microtubules from the cell surface and the subsequent process formation in Sf9 cells. In this system, MAP2b has a lower capacity to induce process formation than MAP2c. To investigate the role of the projection domain in this event, we expressed truncated forms of MAP2b and MAP2c that have partial or complete deletion of their projection domain in Sf9 cells. Our results indicate that process formation is induced by the microtubule-binding domain of these MAP2 proteins and is regulated by their projection domain. Furthermore, the microtubule-binding activity of MAP2b and MAP2c truncated forms as well as the structural properties of the microtubule bundles induced by them do not seem to be the only determinants that control the protrusion of microtubules from the cell surface in Sf9 cells. Rather, our data suggest that microtubule protrusion and process formation are regulated by intramolecular interactions between the projection domain and its microtubule-binding domain in MAP2b.

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The role of the generalized anomeric effect in the conformational analysis of 1,3-dioxacycloalkanes. Conformational analysis of 3,5-dioxabicyclo[5.1.0]octanes and 3,5,8-trioxabicyclo[5.1.0]octanes

The Journal of Organic Chemistry ◽

10.1021/jo00422a050 ◽

1977 ◽

Vol 42 (2) ◽

pp. 365-368 ◽

Cited By ~ 10

Author(s):

Michael H. Gianni ◽

Robert Cody ◽

Mohan R. Asthana ◽

Karl Wursthorn ◽

Patrick Patanode ◽

...

Keyword(s):

Conformational Analysis ◽

Anomeric Effect

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Structure of the 2-isopropylaminoethanol isolated molecule: Conformational analysis and intramolecular interactions

Journal of Molecular Structure THEOCHEM ◽

10.1016/j.theochem.2008.05.028 ◽

2008 ◽

Vol 863 (1-3) ◽

pp. 73-78 ◽

Cited By ~ 4

Author(s):

Sandra C.C. Nunes ◽

M. Ermelinda S. Eusébio ◽

A.J. Lopes Jesus ◽

Mário T.S. Rosado ◽

J.S. Redinha

Keyword(s):

Conformational Analysis ◽

Intramolecular Interactions

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Conformational analysis of 5-lipoxygenase inhibitors: role of the substituents in chiral recognition and on the active conformations of the (methoxyalkyl)thiazole and methoxytetrahydropyran series

Journal of Medicinal Chemistry ◽

10.1021/jm00027a014 ◽

1994 ◽

Vol 37 (1) ◽

pp. 113-124 ◽

Cited By ~ 10

Author(s):

Christine Lambert-van der Brempt ◽

Pierre Bruneau ◽

Maryannick A. Lamorlette ◽

Stephen J. Foster

Keyword(s):

Conformational Analysis ◽

Chiral Recognition ◽

Lipoxygenase Inhibitors

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Structural insights into the role of the Chl4–Iml3 complex in kinetochore assembly

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444913022397 ◽

2013 ◽

Vol 69 (12) ◽

pp. 2412-2419 ◽

Cited By ~ 5

Author(s):

Qiong Guo ◽

Yuyong Tao ◽

Hejun Liu ◽

Maikun Teng ◽

Xu Li

Keyword(s):

De Novo ◽

Molecular Level ◽

Structural Information ◽

Binding Activity ◽

Intramolecular Interactions ◽

Exact Role ◽

Dna Binding Activity ◽

Kinetochore Assembly ◽

Structural Insights

Human CENP-N and CENP-L have been reported to selectively recognize the CENP-A nucleosome and to contribute to recruiting other constitutive centromere-associated network (CCAN) complexes involved in assembly of the inner kinetochore. As their homologues, Chl4 and Iml3 from budding yeast function in a similar way inde novoassembly of the kinetochore. A lack of biochemical and structural information precludes further understanding of their exact role at the molecular level. Here, the crystal structure of Iml3 is presented and the structure shows that Iml3 adopts an elongated conformation with a series of intramolecular interactions. Pull-down assays revealed that the C-terminal domain of Chl4, which forms a dimer in solution, is responsible for Iml3 binding. Acting as a heterodimer, the Chl4–Iml3 complex exhibits a low-affinity nonspecific DNA-binding activity which may play an important role in the kinetochore-assembly process.

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