Salt Bridge in Aqueous Solution: Strong Structural Motifs but Weak Enthalpic Effect

Pylaeva, Svetlana; Brehm, Martin; Sebastiani, Daniel

doi:10.1038/s41598-018-31935-z

Cited by 45 publications

(44 citation statements)

References 45 publications

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“…1A; 1C). Surprisingly, the strong salt bridge between SARS-CoV RBD and hACE2 became a weaker, but still energetically favorable, N-O bridge between Arg439 from the chimeric RBD and Glu329 from hACE2 26 . We measured the binding affinities between the three RBDs (2019-nCoV, chimeric, and SARS-CoV) and hACE2 using surface plasmon resonance assay ( Fig.…”

Section: Resultsmentioning

confidence: 97%

Structural basis for receptor recognition by the novel coronavirus from Wuhan

Shang

Shi

et al. 2020

Preprint

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A novel SARS-like coronavirus (2019-nCoV) recently emerged from Wuhan, China and is quickly spreading in humans. A key to tackling this epidemic is to understand the virus's receptor recognition mechanism, which regulates its infection, pathogenesis, and host range. 2019-nCoV and SARS-CoV recognize the same host receptor ACE2. Here we determined the crystal structure of 2019-nCoV receptor-binding domain (RBD) (engineered to facilitate crystallization) in complex of human ACE2. Compared with SARS-CoV, an ACE2-binding ridge in 2019-nCoV RBD takes more compact conformations, causing structural changes at the RBD/ACE2 interface. Adaptive to these structural changes, several mutations in 2019-nCoV RBD enhance ACE2-binding affinity, contributing to the high infectivity of 2019-CoV. These mutations also reveal the molecular mechanisms of the animal-to-human transmission of 2019-nCoV. Alarmingly, a single N439R mutation in 2019-nCoV RBD further enhances its ACE2-binding affinity, indicating possible future evolution of 2019-nCoV in humans. This study sheds light on the epidemiology and evolution of 2019-nCoV, and provides guidance for intervention strategies targeting receptor recognition by 2019-nCoV.

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Section: Resultsmentioning

confidence: 97%

Structural basis for receptor recognition by the novel coronavirus from Wuhan

Shang

Shi

et al. 2020

Preprint

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“…In a similar vein to the pairing of electrochemically similar residues, oppositely charged residues tended to pair together in electrostatically favorable salt bridges that are known to stabilize protein structures. [45][46][47][48] Such salt bridges represented some of the most enriched amino acid pairings.…”

Section: Amino Acid Contacts Between Strands Favor Stabilizing Interamentioning

confidence: 99%

A systematic analysis of the beta hairpin motif in the Protein Data Bank

DuPai

Davies

Wilke

2020

Preprint

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The beta hairpin motif is a ubiquitous protein structural motif that can be found in molecules across the tree of life. This motif, which is also popular in synthetically designed proteins and peptides, is known for its stability and adaptability to broad functions. Here we systematically probe all 49,000 unique beta hairpin substructures contained within the Protein Data Bank (PDB) to uncover key characteristics correlated with stable beta hairpin structure, including amino acid biases and enriched inter-strand contacts. We also establish a set of broad design principles that can be applied to the generation of libraries encoding proteins or peptides containing beta hairpin structures.

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“…Interestingly, one electrostatic (salt bridge) interaction was noted between E340 of RBD and K2 of jacalin with 5 Å length. The electrostatic interaction is in the acceptable range of medium strength [22]. Besides these interactions, the RBD-jacalin complex was stabilized by van der Waals interaction, and the list of amino acids involved in van der Waals interaction is given in electronic supplementary material, table S2.…”

Section: Resultsmentioning

confidence: 99%