@article {372, title = {Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex.}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {09/2022}, pages = {5138}, chapter = {5138}, abstract = {

Nuclear pore complexes (NPCs) control biomolecular transport in and out of the nucleus. Disordered nucleoporins in the complex{\textquoteright}s pore form a permeation barrier, preventing unassisted transport of large biomolecules. Here, we combine coarse-grained simulations of experimentally derived NPC structures with a theoretical model to determine the microscopic mechanism of passive transport. Brute-force simulations of protein transport reveal telegraph-like behavior, where prolonged diffusion on one side of the NPC is interrupted by rapid crossings to the other. We rationalize this behavior using a theoretical model that reproduces the energetics and kinetics of permeation solely from statistics of transient voids within the disordered mesh. As the protein size increases, the mesh transforms from a soft to a hard barrier, enabling orders-of-magnitude reduction in permeation rate for proteins beyond the percolation size threshold. Our model enables exploration of alternative NPC architectures and sets the stage for uncovering molecular mechanisms of facilitated nuclear transport.

}, keywords = {NPC, nuclear pore, passive transport}, issn = {2041-1723}, doi = {10.1038/s41467-022-32857-1}, author = {Winogradoff, David and Chou, Han-Yi and Maffeo, Christopher and Aleksei Aksimentiev} } @article {324, title = {Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly}, journal = {Nanoscale}, volume = {12}, year = {2020}, month = {02/2020}, pages = {5422--5434}, chapter = {5422}, abstract = {

The effects of detergent sodium dodecyl sulfate (SDS) on protein structure and dynamics are fundamental to the most common laboratory technique used to separate proteins and determine their molecular weights: polyacrylamide gel electrophoresis. However, the mechanism by which SDS induces protein unfolding and the microstructure of protein{\textendash}SDS complexes remain largely unknown. Here, we report a detailed account of SDS-induced unfolding of two proteins{\textemdash}I27 domain of titin and β-amylase{\textemdash}obtained through all-atom molecular dynamics simulations. Both proteins were found to spontaneously unfold in the presence of SDS at boiling water temperature on the time scale of several microseconds. The protein unfolding was found to occur via two distinct mechanisms in which specific interactions of individual SDS molecules disrupt the protein{\textquoteright}s secondary structure. In the final state of the unfolding process, the proteins are found to wrap around SDS micelles in a fluid necklace-and-beads configuration, where the number and location of bound micelles changes dynamically. The global conformation of the protein was found to correlate with the number of SDS micelles bound to it, whereas the number of SDS molecules directly bound to the protein was found to define the relaxation time scale of the unfolded protein. Our microscopic characterization of SDS{\textendash}protein interactions sets the stage for future refinement of SDS{\textendash}enabled protein characterization methods, including protein fingerprinting and sequencing using a solid-state nanopore.

}, doi = {10.1039/c9nr09135a}, author = {David Winogradoff and Shalini John and Aleksei Aksimentiev} } @article {320, title = {Polyhydrazide-based organic nanotubes as extremely efficient and highly selective artificial iodide channels}, journal = {Angewandte Chemie International Edition}, volume = {12}, year = {2020}, month = {02/2020}, pages = {4806-4813}, chapter = {4806}, abstract = {

We report herein a series of pore-containing polymeric nanotubes based on an H-bonded hydrazide backbone. Nanotubes of suitable lengths, possessing a hollow cavity of ~ 6.5 {\r A} in diameter, are found to mediate highly efficient transport of diverse types of anions, rather than cations, across the lipid membrane. Polymer channel 1a, having an averaged molecular weight of 18.2 KDa and 3.6 nm in helical height, exhibits the highest anion transport activities with iodide (EC50 = 0.042 micromolar\ or 0.028 mol \% relative to lipid) being transported 10 times more efficiently than chlorides (EC50 = 0.47 micromolar). Notably, even in the cholesterol-rich environment, iodide transport activity still remains high with EC50\ \ of 0.37 micromolar. Molecular dynamics simulation studies confirm that the channel is highly selective for anions and that such anion selectivity arises from a positive electrostatic potential of the central lumen rendered by the interior-pointing methyl groups.

}, doi = { https://doi.org/10.1002/anie.201916287}, author = {Roy, Arundhati and Joshi, Himanshu and Ye, Ruijuan and Shen, Jie and Chen, Feng and Aleksei Aksimentiev and Zeng, Huaqiang} } @article {290, title = {PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {09/2018}, pages = {3661}, abstract = {

Monodispersed angstrom-size pores embedded in a suitable matrix are promising for highly selective membrane-based separations. They can provide substantial energy savings in water treatment and small molecule bioseparations. Such pores present as membrane proteins (chiefly aquaporin-based) are commonplace in biological membranes but difficult to implement in synthetic industrial membranes and have modest selectivity without tunable selectivity. Here we present PoreDesigner, a design workflow to redesign the robust beta-barrel Outer Membrane Protein F as a scaffold to access three specific pore designs that exclude solutes larger than sucrose (\>360 Da), glucose (\>180 Da), and salt (\>58 Da) respectively. PoreDesigner also enables us to design any specified pore size (spanning 3{\textendash}10 {\r A}), engineer its pore profile, and chemistry. These redesigned pores may be ideal for conducting sub-nm aqueous separations with permeabilities exceeding those of classical biological water channels,\ aquaporins, by more than an order of magnitude at over 10 billion water molecules per channel per second.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06097-1}, url = {https://doi.org/10.1038/s41467-018-06097-1}, author = {Chowdhury, Ratul and Ren, Tingwei and Shankla, Manish and Decker, Karl and Grisewood, Matthew and Prabhakar, Jeevan and Baker, Carol and Golbeck, John H and Aleksei Aksimentiev and Kumar, Manish and Maranas, Costas D} } @inbook {277, title = {A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems}, booktitle = {DNA Nanotechology: Methods and Protocols}, series = {Methods in Molecular Biology}, volume = {1811}, year = {2018}, pages = {209-229}, publisher = {Humana Press}, organization = {Humana Press}, edition = {2}, chapter = {A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems}, address = {New York}, abstract = {

The DNA origami method exploits the self-assembly property of nucleic acids to build diverse nanoscale systems. The all-atom molecular dynamics (MD) method has emerged as a powerful computational tool for atomic-resolution characterization of the in situ structure and physical properties of DNA origami objects. This chapter provides step-by-step instructions for building atomic-scale models of DNA origami systems, using the MD method to simulate the models, and performing basic analyses of the resulting MD trajectories.\ 

}, issn = {978-1-4939-8581-4}, doi = {10.1007/978-1-4939-8582-1_15}, url = {https://link.springer.com/protocol/10.1007/978-1-4939-8582-1_15}, author = {Jejoong Yoo and Chen-Yu Li and Scott Michael Slone and Christopher Maffeo and Aleksei Aksimentiev}, editor = {Giampaolo Zuccheri} } @article {279, title = {Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization}, journal = {ACS Nano}, volume = {11}, year = {2017}, month = {12/2017}, pages = {11931-11945}, abstract = {

Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein. X-ray crystallography, electron microscopy, molecular dynamics and thermal/chaotrope denaturation experiments all find the G20c portal protein to have a highly stable structure, favorable for nanopore sensing applications. Porphyrin conjugation to a cysteine mutant in the protein facilitates the protein{\textquoteright}s insertion into lipid bilayers, allowing us to probe ion transport through the pore. Finally, we probed the portal interior size and shape using a series of cyclodextrins of varying sizes, revealing asymmetric transport that possibly originates from the portal{\textquoteright}s DNA-ratchet function.

}, doi = {10.1021/acsnano.7b06980}, url = {http://pubs.acs.org/doi/abs/10.1021/acsnano.7b06980}, author = {Cressiot*, Benjamin and Greive*, Sandra J. and Si*, Wei and Pascoa, Tomas and Mojtabavi, Mehrnaz and Chechik, Maria and Jenkins, Huw Thomas and Lu, Xueguang and Zhang, Ke and Aleksei Aksimentiev and Antson, Alfred A. and Wanunu, Meni} } @article {258, title = {Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores}, journal = {ACS Nano}, volume = {11}, year = {2017}, month = {07/2017}, pages = {9701-9710}, abstract = {

Nucleic acid nanoparticles (NANPs) are an emerging class of programmable structures with tunable shape and function. Their promise as tools for fundamental biophysics studies, molecular sensing, and therapeutic applications necessitates methods for their detection and characterization at the single-particle level. In this work, we study electrophoretic transport of individual ring-shaped and cube-shaped NANPs through solid-state nanopores. In the optimal nanopore size range, the particles must deform to pass through, which considerably increases their residence time within the pore. Such anomalously long residence times permit detection of picomolar amounts of NANPs when nanopore measurements are carried out at a high transmembrane bias. In the case of a NANP mixture, the type of individual particle passing through nanopores can be efficiently determined from analysis of a single electrical pulse. Molecular dynamics simulations provide insight into the mechanical barrier to transport of the NANPs and corroborate the difference in the signal amplitudes observed for the two types of particles. Our study serves as a basis for label-free analysis of soft programmable-shape nanoparticles.

}, doi = {10.1021/acsnano.7b04923}, url = {http://dx.doi.org/10.1021/acsnano.7b04923}, author = {Alibakhshi, Mohammad Amin and Halman, Justin R. and Wilson, James and Aleksei Aksimentiev and Afonin, Kirill A. and Wanunu, Meni} } @inbook {278, title = {A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems}, booktitle = {Protocols in DNA Nanotechology}, series = {Methods in Molecular Biology}, year = {2017}, publisher = {Humana Press)}, organization = {Humana Press)}, edition = {2nd}, chapter = {A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems} } @article {316, title = {Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones.}, journal = {J Am Chem Soc}, volume = {138}, year = {2016}, month = {10/2016}, pages = {13207-13218}, abstract = {

Histone proteins are essential for the organization, expression, and inheritance of genetic material for eukaryotic cells. A centromere-specific H3 histone variant, centromere protein A (CENP-A), shares about 50\% amino acid sequence identity with H3. CENP-A is required for packaging the centromere and for the proper separation of chromosomes during mitosis. Despite their distinct biological functions, previously reported crystal structures of the CENP-A/H4 and H3/H4 dimers reveal a high degree of similarity. In this work, we characterize the structural dynamics of CENP-A/H4 and H3/H4 dimers based on a dual-resolution approach, using both microsecond-scale explicit-solvent all-atom and coarse-grained (CG) molecular dynamics (MD) simulations. Our data show that the H4 histone is significantly more rigid compared with the H3 histone and its variant CENP-A, hence, serving as a reinforcing structural element within the histone core. We report that the CENP-A/H4 dimer is significantly more dynamic than its canonical counterpart H3/H4, and our results provide a physical explanation for this flexibility. Further, we observe that the centromere-specific chaperone Holliday Junction Recognition Protein (HJURP) stabilizes the CENP-A/H4 dimer by forming a specific electrostatic interaction network. Finally, replacing CENP-A S68 with E68 disrupts the binding interface between CENP-A and HJURP in all-atom MD simulation, and consistently, in vivo experiments demonstrate that replacing CENP-A S68 with E68 disrupts CENP-A{\textquoteright}s localization to the centromere. Based on all our results, we propose that, during the CENP-A/H4 deposition process, the chaperone HJURP protects various substructures of the dimer, serving both as a folding and binding chaperone.

}, keywords = {Centromere Protein A, DNA-Binding Proteins, HeLa Cells, Histones, Humans, Molecular Dynamics Simulation, Protein Folding, Protein Multimerization, Protein Structure, Quaternary, Substrate Specificity}, doi = {10.1021/jacs.6b05355}, author = {Zhao*, Haiqing and Winogradoff*, David and Bui, Minh and Dalal, Yamini and Papoian, Garegin A} } @article {313, title = {Promiscuous histone mis-assembly is actively prevented by chaperones.}, journal = {Journal of the American Chemical Society}, volume = {138}, year = {2016}, pages = {13207--13218}, doi = {10.1021/jacs.6b05355}, author = {Zhao*, Haiqing and Winogradoff*, David and Minh Bui and Yamini Dalal and Garegin Papoian} } @article {204, title = {Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA}, journal = {ACS Nano}, volume = {9}, year = {2015}, month = {09/2015}, pages = {10598--10611}, type = {Article}, abstract = {

\ \ \ \ \ \ With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics\ simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.

}, doi = {10.1021/acsnano.5b04173}, url = {http://pubs.acs.org/doi/10.1021/acsnano.5b04173}, author = {Maxim Belkin and Shu-Han Chao and Magnus P. Jonsson and Cees Dekker and Aleksei Aksimentiev} } @article {29, title = {Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics}, journal = {J Phys Chem C Nanomater Interfaces}, volume = {116}, year = {2012}, month = {2012 Feb 9}, pages = {3376-3393}, abstract = {

It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results of such measurements and to improve the DNA sequence detection method, we have developed a computational approach that has both the atomic-scale accuracy and the computational efficiency required to predict DNA sequence-specific differences in the nanopore ion current. In our Brownian dynamics method, the interaction between the ions and DNA is described by three-dimensional potential of mean force maps determined to a 0.03 nm resolution from all-atom molecular dynamics simulations. While this atomic-resolution Brownian dynamics method produces results with orders of magnitude less computational effort than all-atom molecular dynamics requires, we show here that the ion distributions and ion currents predicted by the two methods agree. Finally, using our Brownian dynamics method, we find that a small change in the sequence of DNA within a pore can cause a large change in the ion current, and validate this result with all-atom molecular dynamics.

}, issn = {1932-7447}, doi = {10.1021/jp210641j}, author = {Jeffrey Comer and Aleksei Aksimentiev} } @article {178, title = {Phase behavior of gradient copolymers}, journal = {The Journal of Chemical Physics}, volume = {111}, year = {1999}, pages = {2329{\textendash}2339}, abstract = {

Phase properties of gradient ABcopolymer melts which consist of chains with the specified chemical distribution of A and B monomers have been studied within the Landau{\textendash}Ginzburg model. All the melts with the linear distribution of the monomers exhibit only a direct continuous phase transition from disordered to the lamellar phase. The hexagonal, body-centered-cubic, double-gyroid (G), and lamellar-ordered structures have been found in the melts with the monotonic but nonlinear distribution of the monomers. The G structure has been also found in the gradient copolymer melts with the distribution function of monomers similar to the A{\textendash}B{\textendash}A triblock copolymers.

}, doi = {10.1063/1.479504}, author = {Aleksei Aksimentiev and Robert Ho{\l}yst} }