Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin–biotin binding

Cong, Yalong; Huang, Kaifang; Li, Yuchen; Zhong, Susu; Zhang, John Z. H.; Duan, Lili

doi:10.1039/c9nr08380d

“…As expected, conformational changes were found in the binding pocket. Furthermore, we observed the minor conformational changes which are less than 1 Å at the residues Ala65, Thr66, Asp77, Ala100, Glu101, Glu116, Ala117, Asp128, Lys132, Val133 and Lys134 correlated with previous mutation studies to elucidate its dynamic application [19,32,33,34,35] (Supplementary Fig. 12a-d) .…”

Section: Resultssupporting

confidence: 82%

Cooperative Allostery and Structural Dynamics of Streptavidin at Cryogenic- and Ambient-temperature

Ayan

¹

,

Yüksel

²

,

Destan

³

et al. 2021

Preprint

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Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

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“…As expected, conformational changes were found in the binding pocket. Furthermore, we observed the minor conformational changes that are <1 Å at the residues Ala65, Thr66, Asp77, Ala100, Glu101, Glu116, Ala117, Asp128, Lys132, Val133, and Lys134 correlated with previous mutation studies to elucidate its dynamic application 19,[32][33][34][35] (Supplementary Fig. 12a-d).…”

Section: Resultssupporting

confidence: 82%

“…There is no certain theoretical definition of this cooperativity in enzymology. The tetrameric structure of streptavidin is known as having the strongest binding affinity found in nature to its substrate biotin and it may thus further contribute to the understanding of cooperativity 18,34,42 . Simultaneous binding of four biotin ligands to streptavidin with full occupancy is unlikely 14 .…”

Section: Discussionmentioning

confidence: 99%

Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature

Ayan

¹

,

Yüksel

²

,

Destan

³

et al. 2022

View full text Add to dashboard Cite

Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

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“…Especially, Asn49 shows the highest individual cooperativity with other residues from the binding pocket to interact with Biotin. 58 To summarize, we obtain the highest rupture force for the system in water, which means that properties. However, the rupture force is lower for CH 3 long monolayer than for CH 3 short.…”

Section: Streptavidin-biotin Unbindingmentioning

confidence: 70%

Impact of Silane Monolayers on the Adsorption of Streptavidin on Silica and Its Subsequent Interactions with Biotin: Molecular Dynamics and Steered Molecular Dynamics Simulations

Lecot

¹

,

Chevolot

²

,

Phaner‐Goutorbe

³

et al. 2020

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Protein adsorption on surfaces is used in analytical tools as an immobilization mean to trap the analyte to be detected. However, protein adsorption can lead to a conformational change in the protein structure, resulting in a loss of bioactivity. Here, we study the adsorption of the Streptavidin -Biotin complex on amorphous SiO 2 surfaces functionalized with five different silane selfassembled monolayers by all-atom Molecular Dynamics simulations. We find that the Streptavidin global conformational change increases linearly with the adsorption energy, which depends, as well as the nature of residues with high mobility, on the alkyl chain length and head group charge of silane molecules. Effects on interactions with Biotin are further investigated by Steered Molecular Dynamics (SMD) simulations, which mimics Atomic Force Microscope (AFM) spectroscopy with the Biotin attached on the tip. We show the combined effects of adsorptioninduced global conformational changes and of the position of residues with high mobility on the force of Biotin detachment. By comparing our results to experimental and SMD detachment forces obtained in water, without any surface, we conclude that silane with uncharged and short alkyl chains allow Streptavidin immobilization, with high adsorption energy, while keeping Biotin interactions better than silanes with long alkyl chains or charged head-groups.

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Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin–biotin binding

Abstract: Molecular dynamics (MD) simulations were performed employing the polarized protein-specific charge (PPC) to explore the origin of the cooperativity in streptavidin–biotin systems (wild type, two single mutations and one double-mutation).

Cited by 24 publications

References 66 publications

Cooperative Allostery and Structural Dynamics of Streptavidin at Cryogenic- and Ambient-temperature

Cooperative Allostery and Structural Dynamics of Streptavidin at Cryogenic- and Ambient-temperature

Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature

Impact of Silane Monolayers on the Adsorption of Streptavidin on Silica and Its Subsequent Interactions with Biotin: Molecular Dynamics and Steered Molecular Dynamics Simulations

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