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Xiao F, Luo L, Liu X, Ljubetič A, Jin N, Jerala R, Hu G. Comparative Simulative Analysis and Design of Single-Chain Self-Assembled Protein Cages. J Phys Chem B 2024. [PMID: 38904939 DOI: 10.1021/acs.jpcb.4c01957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. It represents a type of modular design based on pairwise-interacting coiled-coil (CC) units with a single-chain protein programmed to fold into a polyhedral cage. However, the mechanisms underlying the self-assembly of the protein tetrahedron are still not fully understood. In the present study, 18 CCPO cages with three different topologies were modeled in silico. Then, molecular dynamics simulations and CC parameters were calculated to characterize the dynamic properties of protein tetrahedral cages at both the local and global levels. Furthermore, a deformed CC unit was redesigned, and the stability of the new cage was significantly improved.
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Affiliation(s)
- Fei Xiao
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
| | - Longfei Luo
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
| | - Xin Liu
- Institute of Blood and Marrow Transplantation, Medical College of Soochow University, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, National Clinical Research Center for Hematologic Diseases, Soochow University, Suzhou 215123, China
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Nengzhi Jin
- Key Laboratory of Advanced Computing of Gansu Province, Gansu Computing Center, Lanzhou 730030, China
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Guang Hu
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
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2
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Bai H, Li J, Zhang H, Liu S. Simulative Analysis of a Family of DNA Tetrahedrons Produced by Changing the Twisting Number of Each Double Helix. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, three tetrahedral nanocages, composed of six DNA double helix edges with all having the twist number 1, 2 or 3, have been characterized using classical molecular dynamics simulation to measure the specific structural and conformational features produced by only changing the twisting number of each double helix. The simulation result indicates that three tetrahedral cages are relatively stable and are maintained along the entire trajectory. Each double helix is more inclined to behave as a whole in the 2TD and 3TD cages than in the 1TD cage according to the cross-correlation maps for three nanocages, and also their local motions are more easily induced by the conformational variability of the thymidine linkers due to the increased flexibility of each helix. Hence, the double helices become the important factors on the structural stability of total cages with the DNA twisting number, and also give the signification contributions to the sizes of these cages conferring the larger spaces of the 2TD and 3TD cages than the 1TD cage. Our result provides an insight into which roles the double helix edges play in assembling DNA polyhedron, and also contribute to improving the loading capacity of DNA tetrahedron in drug delivery.
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Affiliation(s)
- Hui Bai
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Jia Li
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Heng Zhang
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Shuya Liu
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan 250100, P. R. China
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3
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Duan J, Cui L, Wang Y, Zheng H. An approach to generate DNA polyhedral links of one/two strands. J Mol Graph Model 2020; 97:107565. [PMID: 32062584 DOI: 10.1016/j.jmgm.2020.107565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 01/30/2023]
Abstract
Scientists can change programmed DNA strands to adjust edge length and vertex junction to control the 3D structures with precision space signatures. The number of strands plays an important role in sequence design, synthesis and constitutive property. However, the majority of DNA branched polyhedra comprise a number of single strands. Therefore, it is crucial to make the number of strands to be calculated as less as possible. DNA polyhedral links are regarded as ideal templates of DNA polyhedra. In this research, we introduce odd-half turn edges and pseudo-surrounded vertexes to build DNA polyhedral links and reduce the strands number of them to one or two. Compare to the known strategies, our strategy is well established to generate the DNA polyhedral links of one/two DNA strands easier and faster. All Platonic, pyramid and prism polyhedral links may provide candidates for DNA polyhedra synthesis.
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Affiliation(s)
- Jinwei Duan
- School of Sciences, Chang'an University, Xi'an, Shaanxi, 710064, PR China.
| | - Lin Cui
- School of Sciences, Chang'an University, Xi'an, Shaanxi, 710064, PR China
| | - Ying Wang
- School of Sciences, Chang'an University, Xi'an, Shaanxi, 710064, PR China
| | - Huayu Zheng
- School of Sciences, Chang'an University, Xi'an, Shaanxi, 710064, PR China
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4
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In Silico and In Cell Analysis of Openable DNA Nanocages for miRNA Silencing. Int J Mol Sci 2019; 21:ijms21010061. [PMID: 31861821 PMCID: PMC6981788 DOI: 10.3390/ijms21010061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/17/2022] Open
Abstract
A computational and experimental integrated approach was applied in order to study the effect of engineering four DNA hairpins into an octahedral truncated DNA nanocage, to obtain a nanostructure able to recognize and bind specific oligonucleotide sequences. Modeling and classical molecular dynamics simulations show that the new H4-DNA nanocage maintains a stable conformation with the closed hairpins and, when bound to complementary oligonucleotides produces an opened conformation that is even more stable due to the larger hydrogen bond number between the hairpins and the oligonucleotides. The internal volume of the open conformation is much larger than the closed one, switching from 370 to 650 nm3, and the predicted larger conformational change is experimentally detectable by gel electrophoresis. H4-DNA nanocages display high stability in serum, can efficiently enter the cells where they are stable and maintain the ability to bind, and sequester an intracellular-specific oligonucleotide. Moreover, H4-DNA nanocages, modified in order to recognize the oncogenic miR21, are able to seize miRNA molecules inside cells in a selective manner.
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5
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Naskar S, Joshi H, Chakraborty B, Seeman NC, Maiti PK. Atomic structures of RNA nanotubes and their comparison with DNA nanotubes. NANOSCALE 2019; 11:14863-14878. [PMID: 31355845 DOI: 10.1039/c9nr00786e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.
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Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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Ottaviani A, Iacovelli F, Idili A, Falconi M, Ricci F, Desideri A. Engineering a responsive DNA triple helix into an octahedral DNA nanostructure for a reversible opening/closing switching mechanism: a computational and experimental integrated study. Nucleic Acids Res 2019; 46:9951-9959. [PMID: 30247614 PMCID: PMC6212788 DOI: 10.1093/nar/gky857] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/19/2018] [Indexed: 11/12/2022] Open
Abstract
We propose an experimental and simulative approach to study the effect of integrating a DNA functional device into a large-sized DNA nanostructure. We selected, as a test bed, a well-known and characterized pH-dependent clamp-switch, based on a parallel DNA triple helix, to be integrated into a truncated octahedral scaffold. We designed, simulated and experimentally characterized two different functionalized DNA nanostructures, with and without the presence of a spacer between the scaffold and the functional elements. The experimental and simulative data agree in validating the need of a spacer for the occurrence of the pH dependent switching mechanism. The system is fully reversible and the switching can be monitored several times without any perturbation, maintaining the same properties of the isolated clamp switch in solution.
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Affiliation(s)
- Alessio Ottaviani
- Biology Department, University of Rome Tor Vergata, Rome 00133, Italy
| | | | - Andrea Idili
- Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy
| | - Mattia Falconi
- Biology Department, University of Rome Tor Vergata, Rome 00133, Italy
| | - Francesco Ricci
- Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy
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Iacovelli F, Cabungcal Hernandez K, Desideri A, Falconi M. Probing the Functional Topology of a pH-Dependent Triple Helix DNA Nanoswitch Family through Gaussian Accelerated MD Simulation. J Chem Inf Model 2019; 59:2746-2752. [PMID: 31074618 DOI: 10.1021/acs.jcim.9b00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The topology of a pH-dependent triple helix DNA nanoswitch family has been characterized through simulative analysis to evaluate the efficiency of the switching mechanism varying the length of the loop connecting the two strands forming the double helix portion. In detail, the system is formed by a double helix made by two six base complementary sequences, connected by one loop having an increasing number of thymidines, namely 5, 7, or 9. The triplex-forming sequence made by six bases, connected to the double helix through a constant 25 base loop, interacts at pH 5.0 through Hoogsteen hydrogen bonds with one strand of the double helical region. We demonstrate, through molecular dynamics simulation, that the thymidine loop length exerts a fine regulatory role for the stability of the triple helix structure and is critical in modulating the switching mechanism triggered by the pH increase.
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Affiliation(s)
- Federico Iacovelli
- Department of Biology, Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB) , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Kevin Cabungcal Hernandez
- Department of Biology, Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB) , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Alessandro Desideri
- Department of Biology, Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB) , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Mattia Falconi
- Department of Biology, Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB) , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
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Shi Z, Castro CE, Arya G. Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. ACS NANO 2017; 11:4617-4630. [PMID: 28423273 DOI: 10.1021/acsnano.7b00242] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically compliant nanostructures with tunable equilibrium conformations and conformational distributions. Here we use coarse-grained molecular dynamics simulations to provide insights into the conformational dynamics of a set of mechanically compliant DNA nanostructures-DNA hinges that use single-stranded DNA "springs" to tune the equilibrium conformation of a layered double-stranded DNA "joint" connecting two stiff "arms" constructed from DNA helix bundles. The simulations reproduce the experimentally measured equilibrium angles between hinge arms for a range of hinge designs. The hinges are found to be structurally stable, except for some fraying of the open ends of the DNA helices comprising the hinge arms and some loss of base-pairing interactions in the joint regions coinciding with the crossover junctions, especially in hinges designed to exhibit a small bending angle that exhibit large local stresses resulting in strong kinks in their joints. Principal component analysis reveals that while the hinge dynamics are dominated by bending motion, some twisting and sliding of hinge arms relative to each other also exists. Forced deformation of the hinges reveals distinct bending mechanisms for hinges with short, inextensible springs versus those with longer, more extensible springs. Lastly, we introduce an approach for rapidly predicting equilibrium hinge angles from individual force-deformation behaviors of its single- and double-stranded DNA components. Taken together, these results demonstrate that coarse-grained modeling is a promising approach for designing, predicting, and studying the dynamics of compliant DNA nanostructures, where conformational fluctuations become important, multiple deformation mechanisms exist, and continuum approaches may not yield accurate properties.
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Affiliation(s)
- Ze Shi
- Department of NanoEngineering, University of California, San Diego , La Jolla, California 92093, United States
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego , La Jolla, California 92093, United States
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9
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Iacovelli F, Idili A, Benincasa A, Mariottini D, Ottaviani A, Falconi M, Ricci F, Desideri A. Simulative and Experimental Characterization of a pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch. J Am Chem Soc 2017; 139:5321-5329. [PMID: 28365993 DOI: 10.1021/jacs.6b11470] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here we couple experimental and simulative techniques to characterize the structural/dynamical behavior of a pH-triggered switching mechanism based on the formation of a parallel DNA triple helix. Fluorescent data demonstrate the ability of this structure to reversibly switch between two states upon pH changes. Two accelerated, half microsecond, MD simulations of the system having protonated or unprotonated cytosines, mimicking the pH 5.0 and 8.0 conditions, highlight the importance of the Hoogsteen interactions in stabilizing the system, finely depicting the time-dependent disruption of the hydrogen bond network. Urea-unfolding experiments and MM/GBSA calculations converge in indicating a stabilization energy at pH 5.0, 2-fold higher than that observed at pH 8.0. These results validate the pH-controlled behavior of the designed structure and suggest that simulative approaches can be successfully coupled with experimental data to characterize responsive DNA-based nanodevices.
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Affiliation(s)
- Federico Iacovelli
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Andrea Idili
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Alessandro Benincasa
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Davide Mariottini
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Alessio Ottaviani
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Mattia Falconi
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Francesco Ricci
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Alessandro Desideri
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
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Joshi H, Bhatia D, Krishnan Y, Maiti PK. Probing the structure and in silico stability of cargo loaded DNA icosahedra using MD simulations. NANOSCALE 2017; 9:4467-4477. [PMID: 28304019 DOI: 10.1039/c6nr08036g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular display with high spatial precision. Therefore high resolution structural models of such polyhedra are critical to widen their applications in both materials and biology. Here, we present an atomistic model of a well-characterized DNA icosahedron, with demonstrated versatile functionalities in biological systems. We study the structure and dynamics of this DNA icosahedron using fully atomistic molecular dynamics (MD) simulation in explicit water and ions. The major modes of internal motion have been identified using principal component analysis. We provide a quantitative estimate of the radius of gyration (Rg), solvent accessible surface area (SASA) and volume of the icosahedron which is essential to estimate its maximal cargo carrying capacity. Importantly, our simulation of gold nanoparticles (AuNPs) encapsulated within DNA icosahedra revealed enhanced stability of the AuNP loaded DNA icosahedra compared to empty icosahedra. This is consistent with the experimental results that show high yields of cargo-encapsulated DNA icosahedra that have led to its diverse applications for precision targeting. These studies reveal that the stabilizing interactions between the cargo and the DNA scaffold powerfully position DNA polyhedra as targetable nanocapsules for payload delivery. These insights can be exploited for precise molecular display for diverse biological applications.
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Affiliation(s)
- Himanshu Joshi
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Dhiraj Bhatia
- Institut Curie, PSL Research University, Chemical Biology of Membranes and Therapeutic Delivery unit, INSERM, U 1143, CNRS, UMR 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA and Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, Illinois 60637, USA
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model. Molecules 2017; 22:molecules22010145. [PMID: 28275219 PMCID: PMC6155889 DOI: 10.3390/molecules22010145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/10/2023] Open
Abstract
DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis. The dynamics profiles derived from ENMs have then been evaluated and compared with previous classical molecular dynamics simulation trajectories. The results presented here revealed that ENMs can provide useful insights into the intrinsic dynamics of large DNA nanocages and represent a useful tool in the field of structural DNA nanotechnology.
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