Real-Time Conformational Changes and Controlled Orientation of Native Proteins Inside a Protein Nanoreactor

Meervelt, Veerle Van; Soskine, Misha; Singh, Shubham; Schuurman-Wolters, Gea K.; Wijma, Hein J.; Poolman, Bert; Maglia, Giovanni

doi:10.1021/jacs.7b10106

Cited by 96 publications

(135 citation statements)

References 46 publications

Supporting

Mentioning

122

Contrasting

Order By: Relevance

“…Detailed knowlegde of the ionic environment can be valuable to experimentalists who seek to trap and study single enzymes with ClyA. 30,97,100 Moreover, it gives insight into the origin of the ion current rectification, ion selectivity and the electro-osmotic flow. We evaluated the densities of both Na We also observed a stark difference between their sensitivities to the applied bias voltage, particularly at low salt concentrations ( Fig.…”

Section: Ion Concentration Distributionmentioning

confidence: 99%

Modeling of Ion and Water Transport in the Biological Nanopore ClyA

Willems

Ruić

Lucas

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

In recent years, the protein nanopore cytolysin A (ClyA) has become a valuable tool for the detection, characterization and quantification of biomarkers, proteins and nucleic acids at the single-molecule level. Despite this extensive experimental utilization, a comprehensive computational study of ion and water transport through ClyA is currently lacking. Such a study yields a wealth of information on the electrolytic conditions inside the pore and on the scale the electrophoretic forces that drive molecular transport. To this end we have built a computationally efficient continuum model of ClyA which, together with an extended version of Poison-Nernst-Planck-Navier-Stokes (ePNP-NS) equations, faithfully reproduces its ionic conductance over a wide range of salt concentrations. These ePNP-NS equations aim to tackle the shortcomings of the traditional PNP-NS models by self-consistently taking into account the influence of both the ionic strength and the nanoscopic scale of the pore on all relevant electrolyte properties. In this study, we give both a detailed description of our ePNP-NS 1 model and apply it to the ClyA nanopore. This enabled us to gain a deeper insight into the influence of ionic strength and applied voltage on the ionic conductance through ClyA and a plethora of quantities difficult to assess experimentally. The latter includes the cation and anion concentrations inside the pore, the shape of the electrostatic potential landscape and the magnitude of the electro-osmotic flow. Our work shows that continuum models of biological nanopores-if the appropriate corrections are applied-can make both qualitatively and quantitatively meaningful predictions that could be valuable tool to aid in both the design and interpretation of nanopore experiments.

show abstract

Section: Ion Concentration Distributionmentioning

confidence: 99%

Modeling of Ion and Water Transport in the Biological Nanopore ClyA

Willems

Ruić

Lucas

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…In the classical induced-fit mechanism 5 , a ligand-free protein is in a single conformation and upon binding of the ligand or substrate, a new conformation is formed. However, nuclear magnetic resonance (NMR) [6][7][8] , electron paramagnetic resonance (EPR) 9 , single-molecule Förster resonance energy transfer (smFRET) [10][11][12][13][14][15][16][17][18][19] and other data [20][21][22] , indicate that proteins sample a range of conformations with and without ligand bound. This led to the notion that, proteins are inherently dynamic and are always in an equilibrium of different conformations 10,[23][24][25] .…”

Section: Introductionmentioning

confidence: 99%

The relation between intrinsic protein conformational changes and ligand binding

Boer

2020

Preprint

View full text Add to dashboard Cite

Structural changes in proteins allow them to exist in several conformations. Non-covalent interactions with ligands drive the structural changes, thereby allowing the protein to perform its biological function.Recent findings suggest that many proteins are always in an equilibrium of different conformations and that each of these conformations can be formed by both the ligand-free and ligand-bound protein. By using classical statistical mechanics, we derived the equilibrium probabilities of forming a conformation with and without ligand. We found, under certain conditions, that increasing the probability of forming a conformation by the ligand-free protein also increases the probability of forming the same conformation when the protein has a ligand bound. Further, we found that changes in the conformational equilibrium of the ligand-free protein can increase or decrease the affinity for the ligand. 2

show abstract

“…[19–22] In a particular study α-hemolysin was used in real-time monitoring of peptide cleavage. [23;24] Other studies utilizing other portals such as Cly A for protein folding, [25;26] Phi29 connector for the distinguish of peptides, [27] and SPP1 connector for peptide oligomerization [28;29] have also been reported.…”

Section: Introductionmentioning

confidence: 99%

Nano-channel of viral DNA packaging motor as single pore to differentiate peptides with single amino acid difference

Kang

Wang

et al. 2018

Biomaterials

View full text Add to dashboard Cite

Detection, differentiation, mapping, and sequencing of proteins are important in proteomics for the assessment of cell development such as protein methylation or phosphorylation as well as the diagnosis of diseases including metabolic disorder, mental illness, immunological ailments, and malignant cancers. Nanopore technology has demonstrated the potential for the sequencing or sensing of DNA, RNA, chemicals, or other macromolecules. Due to the diversity of protein in shape, structure and charge and the composition versatility of 20 amino acids, the sequencing of proteins remains challenging. Herein, we report the application of the channel of bacteriophage T7 DNA packaging motor for the differentiation of an assortment of peptides of a single amino acid difference. Explicit fingerprints or signatures were obtained based on current blockage and dwell time of individual peptide. Data from the clear mapping of small proteins after protease digestion suggests the potential of using T7 motor channel for proteomics including protein sequencing.

show abstract

Real-Time Conformational Changes and Controlled Orientation of Native Proteins Inside a Protein Nanoreactor

Cited by 96 publications

References 46 publications

Modeling of Ion and Water Transport in the Biological Nanopore ClyA

Modeling of Ion and Water Transport in the Biological Nanopore ClyA

The relation between intrinsic protein conformational changes and ligand binding

Nano-channel of viral DNA packaging motor as single pore to differentiate peptides with single amino acid difference

Contact Info

Product

Resources

About