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  • 1. Kang, Yu
    et al.
    Zhang, Zhisen
    Shi, Hui
    Zhang, Junqiao
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Zhejiang University, China .
    Wang, Qi
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Na+ and K+ ion selectivity by size-controlled biomimetic graphene nanopores2014In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 6, no 18, p. 10666-10672Article in journal (Refereed)
    Abstract [en]

    Because biological ionic channels play a key role in cellular transport phenomena, they have attracted extensive research interest for the design of biomimetic nanopores with high permeability and selectivity in a variety of technical applications. Inspired by the structure of K+ channel proteins, we designed a series of oxygen doped graphene nanopores of different sizes by molecular dynamics simulations to discriminate between K+ and Na+ channel transport. The results from free energy calculations indicate that the ion selectivity of such biomimetic graphene nanopores can be simply controlled by the size of the nanopore; compared to K+, the smaller radius of Na+ leads to a significantly higher free energy barrier in the nanopore of a certain size. Our results suggest that graphene nanopores with a distance of about 3.9 A between two neighboring oxygen atoms could constitute a promising candidate to obtain excellent ion selectivity for Na+ and K+ ions.

  • 2.
    Kuang, Guanglin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Zhejiang University, China.
    Brown, Christian
    KTH, School of Biotechnology (BIO), Glycoscience.
    Wang, Qi
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience. Univ Adelaide, Australia.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Insight into the adsorption profiles of the Saprolegnia monoica chitin synthase MIT domain on POPA and POPC membranes by molecular dynamics simulation studies2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 7, p. 5281-5290Article in journal (Refereed)
    Abstract [en]

    The critical role of chitin synthases in oomycete hyphal tip growth has been established. A microtubule interacting and trafficking (MIT) domain was discovered in the chitin synthases of the oomycete model organism, Saprolegnia monoica. MIT domains have been identified in diverse proteins and may play a role in intracellular trafficking. The structure of the Saprolegnia monoica chitin synthase 1 (SmChs1) MIT domain has been recently determined by our group. However, although our in vitro assay identified increased strength in interactions between the MIT domain and phosphatidic acid (PA) relative to other phospholipids including phosphatidylcholine (PC), the mechanism used by the MIT domain remains unknown. In this work, the adsorption behavior of the SmChs1 MIT domain on POPA and POPC membranes was systematically investigated by molecular dynamics simulations. Our results indicate that the MIT domain can adsorb onto the tested membranes in varying orientations. Interestingly, due to the specific interactions between MIT residues and lipid molecules, the binding affinity to the POPA membrane is much higher than that to the POPC membrane. A binding hotspot, which is critical for the adsorption of the MIT domain onto the POPA membrane, was also identified. The lower binding affinity to the POPC membrane can be attributed to the self-saturated membrane surface, which is unfavorable for hydrogen-bond and electrostatic interactions. The present study provides insight into the adsorption profile of SmChs1 and additionally has the potential to improve our understanding of other proteins containing MIT domains.

  • 3.
    Kuang, Guanglin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Brown, Christian
    KTH, School of Biotechnology (BIO), Glycoscience.
    Wang, Qi
    Tu, Yaoquan
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Insight into the adsorption profiles of the Saprolegnia practica chitin synthase MIT domain on POPA and POPC membranes by molecular dynamics simulation studiesManuscript (preprint) (Other academic)
  • 4.
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Computational studies of DNA sequencing with graphene nanopores2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

        The aim of DNA sequencing is to obtain the order of DNA composition comprising the base pairs A (adenine) T (thymine), and C (cytosine) G (guanine). The fast development of DNA sequencing technology allows us to better understand the relationships among diseases, inheritance, and individuality. Solid state nanopores have been recommended as the next generation platform for DNA sequencing due to its low-cost and high-throughput. In particular, nanopores fabricated from graphene sheets are extremely thin and structurally robust and have been extensively used in DNA detection in recent years. In DNA sequencing, the translocation of a DNA molecule through a nanopore is known to be a very complicated issue and is affected by many factors, such as ion concentration, thickness of the nanopore, and the nanopore diameter. The technique of molecular dynamic simulations has been a complementary tool to study DNA translocation through nanopores.  

        In this thesis, I summarize my work of computational studies of DNA sequencing using graphene nanopores. These studies include: DNA translocation through single-layer graphene nanopores of different diameters under conditions of various ion concentrations and applied voltages; DNA translocation through multilayer graphene nanopores varied from a single to a few layers; pulling out single strand DNA molecules from small graphene nanopores of different geometries. The major contributions of this work include:

    1. Effects of bias voltage on DNA translocation time were investigated leading to the insight that lower applied voltages can extend the time of DNA translocation through monolayer graphene nanopores. The effect of salt concentration on the corresponding ionic current was studied. At a low ionic concentration (< 0.3M), the current increases as DNA translocates through a nanopore. However, at a high ionic concentration (>0.5M), the current decreases as DNA translocates through the nanopore. A theoretical model was proposed to explore the relationship between the current and the occupied nanopore area. We demonstrated that the DNA translocation time can be prolonged by narrowing the diameter of a nanopore properly and the reduction of the blockade current depends on the ratio of the unoccupied nanopore area to the total nanopore area.

    2.  DNA translocation through multilayer graphene nanopores was studied by molecular dynamics simulations with the aim to achieve single-base resolution. We show that the DNA translocation time can be extended by increasing the graphene layers up to a moderate number (7) and that the current in DNA translocation undergoes a stepwise change upon DNA going through an multi-layer graphene (MLG) nanopore. A model was built to account for the relationship between the current change and the unoccupied volume of the MLG nanopore. We demonstrate that the blockade current is closely related to the unoccupied volume. The dynamics of DNA translocation depends specifically on the interaction of nucleotides with the graphene sheet. Thus, our study indicates that the resolution of DNA detection can be improved by increasing the number of graphene layers in a certain range and by modifying the surface of graphene nanopores.

    3. The effect of graphene nanopore geometry on DNA sequencing has been assessed by steered molecular dynamics simulations. DNA fragments including A, T, C, G and 5-methylcytosine (MC) were pulled through graphene nanopores of different geometries with diameters down to ~1nm by steered molecular dynamics simulations. We demonstrated that the bases (A, T, C, G, and MC) can be indentified in single-base resolution by the characteristic force peak values in a circular graphene nanopore but not in graphene nanopores of other geometries. Symmetric nanopores are thus better suited to DNA sequence detection via force curves than asymmetric nanopores. This implies that the graphene nanopore surface should be modified as symmetric as possible to sequence DNA by an atomic force microscope or optical tweezers. This helps us to understand low-cost and time-efficient DNA sequencing in narrow nanopores.

    4. The translocation time for different nucleotides to pass through graphene nanopores with certain diameters was investigated. It was found that the translocation times are different for different bases under a low electric field. The results indicate that DNA can be sequenced by the translocation time to pass through a graphene nanopore.

    5. Inspired by the structure of K+ channel proteins, a series of oxygen doped graphene nanopores of different size were designed to discriminate the transport of K+ and Na+ ions. The results indicate that the ion selectivity of such biomimetic graphene nanopores can be simply controlled by the size of the nanopore.  Compared to K+, the smaller radius of Na+ leads to a much higher free energy barrier in the nanopore of a certain size. 

  • 5.
    Liang, Lijun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cui, Peng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, Q.
    Wu, T.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical study on key factors in DNA sequencing with graphene nanopores2013In: RSC Advances, ISSN 2046-2069, Vol. 3, no 7, p. 2445-2453Article in journal (Refereed)
    Abstract [en]

    Solid-state nanopores, in particular graphene nanopores, are believed to have promising applications in DNA sequencing. Many efforts have been made in this research area, the ultimate goal is to extend the DNA translocation time and to achieve single-base resolution. Unfortunately, several factors in DNA sequencing are still not well understood. In this paper, we report a study on the effects of two main factors, the salt concentration and the bias voltage, on the corresponding ionic current. We propose a theoretical model to explore the relationship between the occupied nanopore area and the current. We demonstrate that the DNA translocation time can be prolonged by decreasing the bias voltage and by properly narrowing the nanopore diameter. We find that the reduction of the blockade current depends on the ratio of the unoccupied nanopore area to the total nanopore area.

  • 6.
    Liang, Lijun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kang, Zhengzhong
    Shen, Jia-Wei
    Translocation mechanism of C-60 and C-60 derivations across a cell membrane2016In: Journal of nanoparticle research, ISSN 1388-0764, E-ISSN 1572-896X, Vol. 18, no 11Article in journal (Refereed)
    Abstract [en]

    Carbon-based nanoparticles (NPs) such as fullerenes and nanotubes have been extensively studied for drug delivery in recent years. The permeation process of fullerene and its derivative molecules through membrane is essential to the utilization of fullerene-based drug delivery system, but the mechanism and the dynamics of permeation through cell membrane are still unclear. In this study, coarse-grained molecular dynamics simulations were performed to investigate the permeation process of functionalized fullerene molecules (ca. 0.72 nm) through the membrane. Our results show that single functionalized fullerene molecule in such nanoscale could permeate the lipid membrane in micro-second time scale. Pristine C-60 molecules prefer to aggregate into several small clusters while C60OH15 molecules could aggregate into one big cluster to permeate through the lipid membrane. After permeation of C-60 or its derivatives into membrane, all C-60 and C60OH15 molecules disaggregated and monodispersed in the lipid membrane.

  • 7.
    Liang, Lijun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kong, Zhe
    Kang, Zhengzhong
    Wang, Hongbo
    Zhang, Li
    Shen, Jia-Wei
    Theoretical Evaluation on Potential Cytotoxicity of Graphene Quantum Dots2016In: ACS BIOMATERIALS SCIENCE & ENGINEERING, ISSN 2373-9878, Vol. 2, no 11, p. 1983-1991Article in journal (Refereed)
    Abstract [en]

    Owing to unique morphology, ultrasmall lateral sizes, and exceptional properties, graphene quantum dots (GQDs) hold great potential in many applications, especially in the field of electrochemical biosensors, bioimaging, drug delivery, et cetera. Its biosafety and potential cytotoxicity to human and animal cells has been a growing concern in recent years. In this work, the potential cytotoxicity of GQDs was evaluated by molecular dynamics simulations. Our simulation demonstrates that small size GQDs could easily permeate into the lipid membrane in a vertical way. It is relatively difficult to permeate into the lipid membrane for GQDs that are larger than GQD61 on the nanosecond time-scale. The thickness of the POPC membrane could even be affected by the small size of GQDs. Free energy calculations revealed that the free energy barrier of GQD permeation through the lipid membrane could greatly change with the change of GQD size. Under high GQD concentration, the GQD molecules could rapidly aggregate in water but disaggregate after entering into the membrane interior. Moreover, high concentrations of GQDs could induce changes in the structure properties and diffusion properties of the lipid bilayer, and it may affect the cell signal transduction. However, GQDs with relatively small size are not large enough to mechanically damage the lipid membrane. Our results suggest that the cytotoxicity of GQDs with small size is low and may be appropriate for biomedical application.

  • 8.
    Liang, Lijun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Zhejiang Univ, Peoples R China.
    Wang, Q.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Computational studies of DNA sequencing with solid-state nanopores: Key issues and future prospects2014In: Frontiers in Chemistry, E-ISSN 2296-2646, Vol. 2, no FEB, article id 5Article in journal (Refereed)
    Abstract [en]

    Owing to the potential use for real personalized genome sequencing, DNA sequencing with solid-state nanopores has been investigated intensively in recent time. However, the area still confronts problems and challenges. In this work, we present a brief overview of computational studies of key issues in DNA sequencing with solid-state nanopores by addressing the progress made in the last few years. We also highlight future challenges and prospects for DNA sequencing using this technology.

  • 9.
    Liang, Lijun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Zhejiang University, China.
    Zhang, Zhisen
    Shen, Jiawei
    Zhe, Kong
    Wang, Qi
    Wu, Tao
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical studies on the dynamics of DNA fragment translocation through multilayer graphene nanopores2014In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 4, no 92, p. 50494-50502Article in journal (Refereed)
    Abstract [en]

    Motivated by several potential advantages over common sequencing technologies, solid-state nanopores, in particular graphene nanopores, have recently been extensively explored as biosensor materials for DNA sequencing. Studies carried out on monolayer graphene nanopores aiming at single-base resolution have recently been extended to multilayer graphene (MLG) films, indicating that MLG nanopores are superior to their monolayer counterparts for DNA sequencing. However, the underlying dynamics and current change in the DNA translocation to thread MLG nanopores remain poorly understood. In this paper, we report a molecular dynamics study of DNA passing through graphene nanopores of different layers. We show that the DNA translocation time could be extended by increasing the graphene layers up to a moderate number (7) under a high electric field and that the current in DNA translocation undergoes a stepwise change upon DNA going through an MLG nanopore. A model is built to account for the relationship between the current change and the unoccupied volume of the MLG nanopore. We demonstrate that the dynamics of DNA translocation depends specifically on the interaction of nucleotides with the graphene sheet. Thus, our study indicates that the resolution of DNA detection could be improved by increasing the number of graphene layers in a certain range and by modifying the surface of the graphene nanopores.

  • 10. Shi, Changchun
    et al.
    Kong, Zhe
    Sun, Tianyang
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Department of Chemistry, Soft Matter Research Center, Zhejiang University, China .
    Shen, Jiawei
    Zhao, Zhengyan
    Wang, Qi
    Kang, Zhengzhong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Department of Chemistry, Soft Matter Research Center, Zhejiang University, China.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Molecular dynamics simulations of DNA sequencing with graphene nanopores indicate that DNA bases can be identified by their translocation times2015In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 5, no 13, p. 9389-9395Article in journal (Refereed)
    Abstract [en]

    The improvement of the resolution of DNA sequencing by nanopore technology is very important for its real-life application. In this paper, we report our work on using molecular dynamics simulation to study the dependence of DNA sequencing on the translocation time of DNA through a graphene nanopore, using the single-strand DNA fragment translocation through graphene nanopores with diameters down to similar to 2 nm as examples. We found that A, T, C, and G could be identified by the difference in the translocation time between different types of nucleotides through 2 nm graphene nanopores. In particular, the recognition of the graphene nanopore for different nucleotides can be greatly enhanced in a low electric field. Our study suggests that the recognition of a graphene nanopore by different nucleotides is the key factor for sequencing DNA by translocation time. Our study also indicates that the surface of a graphene nanopore can be modified to increase the recognition of nucleotides and to improve the resolution of DNA sequencing based on the DNA translocation time with a suitable electric field.

  • 11. Shi, Changchun
    et al.
    Zhe, Kong
    Sun, Tianyang
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Zhejiang University, China.
    Shen, Jiawei
    Zhao, Zhengyan
    Wang, Qi
    Kang, Zhengzhong
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Sequence dependence on DNA translocation time by graphene nanoporeManuscript (preprint) (Other academic)
  • 12. Zhang, Junqiao
    et al.
    Li, Debing
    Sun, Tianyang
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Zhejiang University, China.
    Wang, Qi
    Interaction of P-glycoprotein with anti-tumor drugs: the site, gate and pathway2015In: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 11, no 33, p. 6633-6641Article in journal (Refereed)
    Abstract [en]

    Understanding the mechanism and pathway of anti-cancer drugs to be pumped out by P-glycoprotein (P-gp) in cancer cell is very important for the successful chemotherapy. P-gp is a member of ATP-binding cassette (ABC) transporters. In this study, random accelerated molecular dynamics (RAMD) simulation was used to explore the potential egress pathway of ligands from the binding pocket. This could be considered as a reverse process of drug binding. The most possible portal of drugs to dissociate is TM4/TM6, which is almost the same for different drugs, such as paclitaxel and doxorubicin. The interactions in the binding site are found to be remarkably stronger than that outside of the binding site. The results were suggested by the free energy calculation between P-gp and different drugs from metadynamics simulation. All the results indicate that the flexibility of inner residues, especially the residue Phe339, is very important for the drugs to access the binding site.

  • 13. Zhang, Zhisen
    et al.
    Shen, Jiawei
    Wang, Hongbo
    Wang, Qi
    Zhang, Junqiao
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Effects of Graphene Nanopore Geometry on DNA Sequencing2014In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 5, no 9, p. 1602-1607Article in journal (Refereed)
    Abstract [en]

    In this Letter we assess the effect of graphene nanopore geometries on DNA sequencing by considering DNA fragments including A, T, C, G, and 5-methylcytosine (MC) pulled out of graphene nanopores of different geometries with diameters down to similar to 1 nm. Using steered molecular dynamics simulations it is demonstrated that the bases (A, T, C, G, and MC) can be indentified at single-base resolution through the characteristic peaks on the force profile in a circular graphene nanopore but not in nanopores with other asymmetric geometries. Our study suggests that the graphene nanopore surface should be modified as symmetrically as possible in order to sequence DNA by atomic force microscopy or optical tweezers.

1 - 13 of 13
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