Essentials of biorecognition: The (strept)avidin–biotin system as a model for protein–protein and protein–ligand interaction

Wilchek, Meir; Bayer, Edward A.; Livnah, Oded

doi:10.1016/j.imlet.2005.10.022

Cited by 206 publications

(146 citation statements)

References 41 publications

(55 reference statements)

Supporting

Mentioning

141

Contrasting

Unclassified

Order By: Relevance

“…Rather, it is an additional contribution to the forces acting at short distance that can enhance the affinity and are intrinsically enantioselective. It has long been known that the current physical models used to describe the interaction between biological molecules do not properly account for the enantioselectivity and binding energies in biorecognition (2)(3)(4)(5). In the past, this gap was filled using empirically based methods (34).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Chirality-induced spin polarization places symmetry constraints on biomolecular interactions

Kumar

Capua

Kesharwani

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

170

230

View full text Add to dashboard Cite

Noncovalent interactions between molecules are key for many biological processes. Necessarily, when molecules interact, the electronic charge in each of them is redistributed. Here, we show experimentally that, in chiral molecules, charge redistribution is accompanied by spin polarization. We describe how this spin polarization adds an enantioselective term to the forces, so that homochiral interaction energies differ from heterochiral ones. The spin polarization was measured by using a modified Hall effect device. An electric field that is applied along the molecules causes charge redistribution, and for chiral molecules, a Hall voltage is measured that indicates the spin polarization. Based on this observation, we conjecture that the spin polarization enforces symmetry constraints on the biorecognition process between two chiral molecules, and we describe how these constraints can lead to selectivity in the interaction between enantiomers based on their handedness. Model quantum chemistry calculations that rigorously enforce these constraints show that the interaction energy for methyl groups on homochiral molecules differs significantly from that found for heterochiral molecules at van der Waals contact and shorter (i.e., ∼0.5 kcal/mol at 0.26 nm).spin | chirality | enantioselectivity | biorecognition | exchange interaction T he wealth of information on protein structure has led to a much better understanding of the relation between structure and function in biomolecular processes and biological machines (1); however, basic phenomena remain unexplained in terms of structure-function relationships. Biorecognition, which is based on noncovalent interactions between molecules, retains mysteries, and its calculation evades first principles theory (2, 3). This failure suggests that some essential features are not included in our current description of these interactions (4,5). In this study, we show that charge polarization, which occurs in any biorecognition event, is accompanied by spin polarization for chiral molecules, an effect that is missing in most treatments. The subsequent magnetic interaction energies are small and therefore, play no significant role in the interactions; however, the spin polarization constrains the symmetry of the wave function(s) involved with the intermolecular interaction, so that significant differences in energy emerge for interactions between molecules of the same chirality and those of opposite chirality. Thus, this phenomenon may impact quantitative modeling of biorecognition events and contribute to our understanding of enantiorecognition in nature (6).Nucleotides, amino acids, and sugars are chiral; namely, they do not possess mirror plane symmetry but have symmetry like a "hand" (cheir in Greek). Force field models for the interaction between biomolecules do not account for spin polarization or include terms with chiral symmetry. Noncovalent interactions between biomolecules are commonly described classically by way of force fields, which are constructed from their geometrie...

show abstract

Section: Discussionmentioning

confidence: 99%

“…Biorecognition, which is based on noncovalent interactions between molecules, retains mysteries, and its calculation evades first principles theory (2,3). This failure suggests that some essential features are not included in our current description of these interactions (4,5).…”

mentioning

confidence: 99%

Chirality-induced spin polarization places symmetry constraints on biomolecular interactions

Kumar

Capua

Kesharwani

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

170

230

View full text Add to dashboard Cite

show abstract

“…The biotin-binding proteins, namely, chicken egg-white avidin, bacterial streptavidin and newly discovered tamavidins from basidiomycete fungi, have numerous medical, biological, biochemical and biotechnological applications (Laitinen et al, 2006;Takakura et al, 2010;Wilchek et al, 2006). These tetrameric proteins, consisting of classical -barrel monomers, bind biotin with exceptionally high affinity.…”

Section: Diversity Of Ligand-binding Proteinsmentioning

confidence: 99%

Ligand-Binding Proteins: Structure, Stability and Practical Application

Stepanenko¹,

Fonin²,

Stepanenko³

et al. 2012

Protein Structure

View full text Add to dashboard Cite

“…Streptavidin forms tetramers with four high affinity binding sites for biotin and is often used to link biotinylated molecules. 8 We use a ratio between 50:1 and 100:1 non-biotinylated to biotinylated PEG in our reaction mixture. This ratio gives tens to hundreds of tethered DNAs in the microscope's field of view.…”

Section: A Dna Tetheringmentioning

confidence: 99%

A single molecule DNA flow stretching microscope for undergraduates

Williams

Grafe

Burke

et al. 2011

American Journal of Physics

View full text Add to dashboard Cite

The design of a simple, safe, and inexpensive single molecule flow stretching instrument is presented. The instrument uses a low cost upright microscope coupled to a webcam for imaging single DNA molecules that are tethered in an easy to construct microfluidic flow cell. The system requires no special vibration isolation and is capable of measuring DNA replication at the single molecule level. We discuss two laboratory experiments suitable for advanced undergraduates using our microscope.

show abstract

Essentials of biorecognition: The (strept)avidin–biotin system as a model for protein–protein and protein–ligand interaction

Cited by 206 publications

References 41 publications

Chirality-induced spin polarization places symmetry constraints on biomolecular interactions

Chirality-induced spin polarization places symmetry constraints on biomolecular interactions

Ligand-Binding Proteins: Structure, Stability and Practical Application

A single molecule DNA flow stretching microscope for undergraduates

Contact Info

Product

Resources

About