scholarly journals An interesting possibility of forming special hole stepping stones with high-stacking aromatic rings in proteins: three-π five-electron and four-π seven-electron resonance bindings

RSC Advances ◽  
2021 ◽  
Vol 11 (43) ◽  
pp. 26672-26682
Author(s):  
Xin Li ◽  
Weichao Sun ◽  
Xin Qin ◽  
Yuxin Xie ◽  
Nian Liu ◽  
...  
Keyword(s):  
Close Approach ◽  
Side Chains ◽  
Biological Processes ◽  
Aromatic Rings ◽  
Stepping Stones ◽  
Long Distance ◽  
Hole Transfer ◽  
Electron Resonance ◽  
Interesting Possibility ◽  
Aromatic Side Chains

The three-π five-electron relay forming by three close approach aromatic side chains may promote hole transfer in proteins, supporting hole translocation across a long distance during sophisticated biological processes.

Packing of aromatic rings against tryptophan residues in proteins

1999 ◽  
Vol 55 (8) ◽  
pp. 1421-1427 ◽  
Author(s):  
Uttamkumar Samanta ◽  
Debnath Pal ◽  
Pinak Chakrabarti
Keyword(s):  
Protein Data Bank ◽  
Chemical Nature ◽  
Data Bank ◽  
Side Chains ◽  
Indole Ring ◽  
Aromatic Rings ◽  
Dominant Feature ◽  
Tryptophan Residues ◽  
Uniform Manner ◽  
Aromatic Side Chains

The geometry of the interaction of the aromatic side chains of phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp) and histidine (His) with the indole ring of Trp has been analyzed using the structures in the Protein Data Bank in order to understand the dependence of the packing behaviour on the size and chemical nature of the aromatic rings. The Phe ring prefers to interact either perpendicularly, with its edge pointing towards the Trp face, or in an offset-stacked arrangement. The edge-to-face motif is typical of a Trp–Trp pair. While parallel stacking is the dominant feature of Trp–His interaction, Tyr packs in a more uniform manner around Trp with a higher than expected occurrence at the edge and a few cases of possible OH–π interaction.

Influence of Amino Acid Side Chains on Long-Distance Electron Transfer in Peptides: Electron Hopping via “Stepping Stones”

2008 ◽  
Vol 47 (18) ◽  
pp. 3461-3463 ◽  
Author(s):  
Meike Cordes ◽  
Angnieszka Köttgen ◽  
Christian Jasper ◽  
Olivier Jacques ◽  
Hassen Boudebous ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Amino Acid ◽  
Side Chains ◽  
Stepping Stones ◽  
Long Distance ◽  
Electron Hopping ◽  
Amino Acid Side Chains

Privileged hydration sites in aromatic side chains: effect on conformational equilibrium

2017 ◽  
Vol 19 (42) ◽  
pp. 28684-28695 ◽  
Author(s):  
Belén Hernández ◽  
Fernando Pflüger ◽  
Manuel Dauchez ◽  
Mahmoud Ghomi
Keyword(s):  
Conformational Equilibrium ◽  
Theoretical Calculations ◽  
Side Chains ◽  
Aromatic Side Chains

The most energetically favourable hydration sites of aromatic (Phe, Tyr, Trp and His) side chains revealed by DFT-based theoretical calculations.

scholarly journals Global biogeographic patterns in bipolar moss species

2017 ◽  
Vol 4 (7) ◽  
pp. 170147 ◽  
Author(s):  
E. M. Biersma ◽  
J. A. Jackson ◽  
J. Hyvönen ◽  
S. Koskinen ◽  
K. Linse ◽  
...  
Keyword(s):  
Large Scale ◽  
Common Species ◽  
Long Distance Dispersal ◽  
Stepping Stones ◽  
Long Distance ◽  
Antarctic Region ◽  
Moss Species ◽  
Biogeographic Patterns ◽  
Biogeographic Pattern ◽  
The Antarctic

A bipolar disjunction is an extreme, yet common, biogeographic pattern in non-vascular plants, yet its underlying mechanisms (vicariance or long-distance dispersal), origin and timing remain poorly understood. Here, combining a large-scale population dataset and multiple dating analyses, we examine the biogeography of four bipolar Polytrichales mosses, common to the Holarctic (temperate and polar Northern Hemisphere regions) and the Antarctic region (Antarctic, sub-Antarctic, southern South America) and other Southern Hemisphere (SH) regions. Our data reveal contrasting patterns, for three species were of Holarctic origin, with subsequent dispersal to the SH, while one, currently a particularly common species in the Holarctic ( Polytrichum juniperinum ), diversified in the Antarctic region and from here colonized both the Holarctic and other SH regions. Our findings suggest long-distance dispersal as the driver of bipolar disjunctions. We find such inter-hemispheric dispersals are rare, occurring on multi-million-year timescales. High-altitude tropical populations did not act as trans-equatorial ‘stepping-stones’, but rather were derived from later dispersal events. All arrivals to the Antarctic region occurred well before the Last Glacial Maximum and previous glaciations, suggesting that, despite the harsh climate during these past glacial maxima, plants have had a much longer presence in this southern region than previously thought.

scholarly journals Free Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitor Using Metadynamics

2021 ◽  
Author(s):  
Pär Söderhjelm ◽  
Mandar Kulkarni
Keyword(s):  
Free Energy ◽  
Trypsin Inhibitor ◽  
Side Chain ◽  
Side Chains ◽  
Aromatic Residues ◽  
Basic Pancreatic Trypsin Inhibitor ◽  
Pancreatic Trypsin Inhibitor ◽  
Energy Surfaces ◽  
Aromatic Side Chains

Aromatic side-chains (phenylalanine and tyrosine) of a protein flip by 180° around the Cβ-Cγ axis (χ2 dihedral of side-chain) producing two symmetry-equivalent states. The ring-flip dynamics act as an NMR probe to understand local conformational fluctuations. Ring-flips are categorized as slow (ms onwards) or fast (ns to near ms) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to discriminate between slow and fast ring-flips for eight individual aromatic side-chains (F4, Y10, Y21, F22, Y23, F33, Y35, F45) of basic pancreatic trypsin inhibitor (BPTI). Well-tempered metadynamics simulations were performed to observe ring-flipping free energy surfaces for all eight aromatic residues. The results indicate that χ2 as a standalone collective variable (CV) is not sufficient to classify fast and slow ring-flips. Most of the residues needed χ1 (N−Cχα) as a complementary CV, indicating the importance of librational motions in ring-flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events are observed for residues F22 and F33, indicating a possible role of friction effects in the ring-flipping. The results demonstrate the successful application of the metadynamics based approach to estimate ring-flip rates of aromatic residues in BPTI and identify certain limitations of the approach.

Biosynthetic13C Labeling of Aromatic Side Chains in Proteins for NMR Relaxation Measurements

2006 ◽  
Vol 128 (8) ◽  
pp. 2506-2507 ◽  
Author(s):  
Kaare Teilum ◽  
Ulrika Brath ◽  
Patrik Lundström ◽  
Mikael Akke
Keyword(s):  
Nmr Relaxation ◽  
Side Chains ◽  
Relaxation Measurements ◽  
Aromatic Side Chains

scholarly journals Protein Native-State Stabilization by Placing Aromatic Side Chains in N-Glycosylated Reverse Turns

Science ◽  
2011 ◽  
Vol 331 (6017) ◽  
pp. 571-575 ◽  
Author(s):  
E. K. Culyba ◽  
J. L. Price ◽  
S. R. Hanson ◽  
A. Dhar ◽  
C.-H. Wong ◽  
...  
Keyword(s):  
Side Chains ◽  
Native State ◽  
Aromatic Side Chains
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