[논문]High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities

Bryer, Alexander J.; Hadden-Perilla, Jodi A.; Stone, John E.; Perilla, Juan R.

doi:10.1021/acs.jcim.9b00324

[해외논문] High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities 원문보기

Journal of chemical information and modeling, v.59 no.10, 2019년, pp.4328 - 4338

Bryer, Alexander J. (Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States) , Hadden-Perilla, Jodi A. (Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States) , Stone, John E. (Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana−) , Perilla, Juan R. (Champaign , Urbana , Illinois 61801 , United States)

Abstract ▼ AI-Helper

Compartmentalization is a central theme in biology. Cells are composed of numerous membrane-enclosed structures, evolved to facilitate specific biochemical processes; viruses act as containers of genetic material, optimized to drive infection. Molecular dynamics simulations provide a mechanism to study biomolecular containers and the influence they exert on their environments; however, trajectory analysis software generally lacks knowledge of container interior versus exterior. Further, many relevant container analyses involve large-scale particle tracking endeavors, which may become computationally prohibitive with increasing system size. Here, a novel method based on 3-D ray casting is presented, which rapidly classifies the space surrounding biomolecular containers of arbitrary shape, enabling fast determination of the identities and counts of particles (e.g., solvent molecules) found inside and outside. The method is broadly applicable to the study of containers and enables high-performance characterization of properties such as solvent density, small-molecule transport, transbilayer lipid diffusion, and topology of protein cavities. The method is implemented in VMD, a widely used simulation analysis tool that supports personal computers, clouds, and parallel supercomputers, including ORNL’s Summit and Titan and NCSA’s Blue Waters, where the method can be employed to efficiently analyze trajectories encompassing millions of particles. The ability to rapidly characterize the spatial relationships of particles relative to a biomolecular container over many trajectory frames, irrespective of large particle counts, enables analysis of containers on a scale that was previously unfeasible, at a level of accuracy that was previously unattainable.[FIG OMISSION]

참고문헌 (58)

Contreras, F.-Xabier, Sánchez-Magraner, Lissete, Alonso, Alicia, Goñi, Félix M.. Transbilayer (flip-flop) lipid motion and lipid scrambling in membranes. FEBS letters, vol.584, no.9, 1779-1786.

상세보기
Daleke, David L.. Regulation of transbilayer plasma membrane phospholipid asymmetry. Journal of lipid research, vol.44, no.2, 233-242.

상세보기
Fattal, Elias, Nir, Shlomo, Parente, Roberta A., Szoka Jr., Francis C.. Pore-Forming Peptides Induce Rapid Phospholipid Flip-Flop in Membranes. Biochemistry, vol.33, no.21, 6721-6731.

상세보기
Perilla, J.R., Goh, B.C., Cassidy, C.K., Liu, B., Bernardi, R.C., Rudack, T., Yu, H., Wu, Z., Schulten, K.. Molecular dynamics simulations of large macromolecular complexes. Current opinion in structural biology, vol.31, 64-74.

상세보기
Hadden, Jodi A, Perilla, Juan R. All-atom virus simulations. Current Opinion in Virology, vol.31, 82-91.

상세보기
Reddy, Tyler, Sansom, Mark S.P.. Computational virology: From the inside out ^☆. Biochimica et biophysica acta, Biomembranes, vol.1858, no.7, 1610-1618.

상세보기
Marrink, S. J., Mark, A. E.. The Mechanism of Vesicle Fusion as Revealed by Molecular Dynamics Simulations. Journal of the American Chemical Society, vol.125, no.37, 11144-11145.

상세보기
Marrink, S. J., Mark, A. E.. Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles. Journal of the American Chemical Society, vol.125, no.49, 15233-15242.

상세보기
Knecht, V., Marrink, S.J.. Molecular Dynamics Simulations of Lipid Vesicle Fusion in Atomic Detail. Biophysical journal, vol.92, no.12, 4254-4261.

상세보기
Wu, Shaogui, Guo, Hongxia. Simulation Study of Protein-Mediated Vesicle Fusion. The journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, vol.113, no.3, 589-591.

상세보기
Hofsasz, C., Lindahl, E., Edholm, O.. Molecular Dynamics Simulations of Phospholipid Bilayers with Cholesterol. Biophysical journal, vol.84, no.4, 2192-2206.

상세보기
Braun, Anthony R., Sachs, Jonathan N.. Determining Structural and Mechanical Properties from Molecular Dynamics Simulations of Lipid Vesicles. Journal of chemical theory and computation, vol.10, no.9, 4160-4168.

상세보기
Perilla, Juan R., Schulten, Klaus. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations. Nature communications, vol.8, 15959-.

상세보기
Hadden, Jodi A, Perilla, Juan R, Schlicksup, Christopher John, Venkatakrishnan, Balasubramanian, Zlotnick, Adam, Schulten, Klaus. All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits. eLife, vol.7, e32478-.

상세보기
Humphrey, W., Dalke, A., Schulten, K.. VMD: Visual molecular dynamics. Journal of molecular graphics, vol.14, no.1, 33-38.

상세보기
10.1109/IPDPSW.2010.5470898 Phillips, M.; Georgiev, I.; Dehof, A. K.; Nickels, S.; Marsalek, L.; Lenhof, H. P.; Hildebrandt, A.; Slusallek, P. Measuring Properties of Molecular Surfaces Using Ray Casting. In 2010 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW) ; IEEE, 2010; pp 1-7.
Eurographics Amanatides J. 3 87 1987
10.1145/1278780.1278807
EuroVis - Short Papers Krone M. 67 2012 2012
Proceedings of the 8th International Workshop on Ultrascale Visualization Stone J. E. 6:1 2013
Larson, S.B., Day, J., Greenwood, A., McPherson, A.. Refined structure of satellite tobacco mosaic virus at 1.8 A resolution. Journal of molecular biology, vol.277, no.1, 37-59.

상세보기
Bourne, Christina R., Finn, M. G., Zlotnick, Adam. Global Structural Changes in Hepatitis B Virus Capsids Induced by the Assembly Effector HAP1. Journal of virology, vol.80, no.22, 11055-11061.

상세보기
Sirohi, Devika, Chen, Zhenguo, Sun, Lei, Klose, Thomas, Pierson, Theodore C., Rossmann, Michael G., Kuhn, Richard J.. The 3.8 Å resolution cryo-EM structure of Zika virus. Science, vol.352, no.6284, 467-470.

상세보기
Stehle, Thilo, Gamblin, Steven J, Yan, Youwei, Harrison, Stephen C. The structure of simian virus 40 refined at 3.1 å resolution. Structure, vol.4, no.2, 165-182.

상세보기
Zhao, Gongpu, Perilla, Juan R., Yufenyuy, Ernest L., Meng, Xin, Chen, Bo, Ning, Jiying, Ahn, Jinwoo, Gronenborn, Angela M., Schulten, Klaus, Aiken, Christopher, Zhang, Peijun. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature, vol.497, no.7451, 643-646.

상세보기
10.1002/(SICI)1096-987X(19980730)19:10<1179::AID-JCC6>3.0.CO;2-J

상세보기
Perilla, Juan R., Zhao, Gongpu, Lu, Manman, Ning, Jiying, Hou, Guangjin, Byeon, In-Ja L., Gronenborn, Angela M., Polenova, Tatyana, Zhang, Peijun. CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. The journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, vol.121, no.15, 3853-3863.

상세보기
Fuller, Derek N., Rickgauer, John Peter, Jardine, Paul J., Grimes, Shelley, Anderson, Dwight L., Smith, Douglas E.. Ionic effects on viral DNA packaging and portal motor function in bacteriophage φ29. Proceedings of the National Academy of Sciences of the United States of America, vol.104, no.27, 11245-11250.

상세보기
Nap, Rikkert J., Božič, Anže Lošdorfer, Szleifer, Igal, Podgornik, Rudolf. The Role of Solution Conditions in the Bacteriophage PP7 Capsid Charge Regulation. Biophysical journal, vol.107, no.8, 1970-1979.

상세보기
Andoh, Y., Yoshii, N., Yamada, A., Fujimoto, K., Kojima, H., Mizutani, K., Nakagawa, A., Nomoto, A., Okazaki, S.. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution. The Journal of chemical physics, vol.141, no.16, 165101-.

상세보기
van Meer, Gerrit, Voelker, Dennis R., Feigenson, Gerald W.. Membrane lipids: where they are and how they behave. Nature reviews. Molecular cell biology, vol.9, no.2, 112-124.

상세보기
Allhusen, John S., Conboy, John C.. The Ins and Outs of Lipid Flip-Flop. Accounts of chemical research, vol.50, no.1, 58-65.

상세보기
Eriksson, AE, Baase, WA, Zhang, XJ, Heinz, DW, Blaber, M, Baldwin, EP, Matthews, BW. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science, vol.255, no.5041, 178-183.

상세보기
Ohmura, Tadahiro, Ueda, Tadashi, Ootsuka, Keiichi, Saito, Minoru, Imoto, Taiji. Stabilization of hen egg white lysozyme by a cavity‐filling mutation. Protein science : a publication of the Protein Society, vol.10, no.2, 313-320.

상세보기
Brunori, Maurizio, Vallone, Beatrice, Cutruzzolà, Francesca, Travaglini-Allocatelli, Carlo, Berendzen, Joel, Chu, Kelvin, Sweet, Robert M., Schlichting, Ilme. The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin. Proceedings of the National Academy of Sciences of the United States of America, vol.97, no.5, 2058-2063.

상세보기
Pace, C. Nick, Shirley, Bret A., McNutt, Marsha, Gajiwala, Ketan. Forces contributing to the conformational stability of proteins. The FASEB journal : official publication of the Federation of American Societies for Experimental Biology, vol.10, no.1, 75-83.

상세보기
Computer Graphics Forum Krone M. 527 35 2016
Durrant, Jacob D., de Oliveira, César Augusto F., McCammon, J. Andrew. POVME: An algorithm for measuring binding-pocket volumes. Journal of molecular graphics & modelling, vol.29, no.5, 773-776.

상세보기
Durrant, Jacob D., Votapka, Lane, Sørensen, Jesper, Amaro, Rommie E.. POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. Journal of chemical theory and computation, vol.10, no.11, 5047-5056.

상세보기
Wagner, Jeffrey R., Sørensen, Jesper, Hensley, Nathan, Wong, Celia, Zhu, Clare, Perison, Taylor, Amaro, Rommie E.. POVME 3.0: Software for Mapping Binding Pocket Flexibility. Journal of chemical theory and computation, vol.13, no.9, 4584-4592.

상세보기
Le Guilloux, Vincent, Schmidtke, Peter, Tuffery, Pierre. Fpocket: An open source platform for ligand pocket detection. BMC bioinformatics, vol.10, 168-168.

상세보기
Schmidtke, Peter, Le Guilloux, Vincent, Maupetit, Julien, Tufféry, Pierre. fpocket: online tools for protein ensemble pocket detection and tracking. Nucleic acids research, vol.38, no.2, W582-W589.

상세보기
Schmidtke, Peter, Bidon-Chanal, Axel, Luque, F. Javier, Barril, Xavier. MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories. Bioinformatics, vol.27, no.23, 3276-3285.

상세보기
Kokh, Daria B., Richter, Stefan, Henrich, Stefan, Czodrowski, Paul, Rippmann, Friedrich, Wade, Rebecca C.. TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins. Journal of chemical information and modeling, vol.53, no.5, 1235-1252.

상세보기
Stank, Antonia, Kokh, Daria B., Horn, Max, Sizikova, Elena, Neil, Rebecca, Panecka, Joanna, Richter, Stefan, Wade, Rebecca C.. TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets. Nucleic acids research, vol.45, no.w1, W325-W330.

상세보기
Laurent, Benoist, Chavent, Matthieu, Cragnolini, Tristan, Dahl, Anna Caroline E., Pasquali, Samuela, Derreumaux, Philippe, Sansom, Mark S.P., Baaden, Marc. Epock: rapid analysis of protein pocket dynamics. Bioinformatics, vol.31, no.9, 1478-1480.

상세보기
Desaphy, Jérémy, Azdimousa, Karima, Kellenberger, Esther, Rognan, Didier. Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes. Journal of chemical information and modeling, vol.52, no.8, 2287-2299.

상세보기
Paramo, Teresa, East, Alexandra, Garzón, Diana, Ulmschneider, Martin B., Bond, Peter J.. Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity. Journal of chemical theory and computation, vol.10, no.5, 2151-2164.

상세보기
Proc. Natl. Acad. Sci. U. S. A. Roche J. 6945 109 2012 10.1073/pnas.1200915109

상세보기
Maurer-Stroh, Sebastian, Ma, Jianmin, Lee, Raphael Tze Chuen, Sirota, Fernanda L, Eisenhaber, Frank. Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites. Biology direct, vol.4, 18-18.

상세보기
Tantillo, C., Ding, J., Jacobo-Molina, A., Nanni, R.G., Boyer, P.L., Hughes, S.H., Pauwels, R., Andries, K., Janssen, P.A.J., Arnold, E.. Locations of Anti-AIDS Drug Binding Sites and Resistance Mutations in the Three-dimensional Structure of HIV-1 Reverse Transcriptase - Implications for Mechanisms of Drug Inhibition and Resistance. Journal of molecular biology, vol.243, no.3, 369-387.

상세보기
Yun, Cai-Hong, Mengwasser, Kristen E., Toms, Angela V., Woo, Michele S., Greulich, Heidi, Wong, Kwok-Kin, Meyerson, Matthew, Eck, Michael J.. The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP. Proceedings of the National Academy of Sciences of the United States of America, vol.105, no.6, 2070-2075.

상세보기
Castañeda, Carlos A., Fitch, Carolyn A., Majumdar, Ananya, Khangulov, Victor, Schlessman, Jamie L., García-Moreno, Bertrand E.. Molecular determinants of the pK_a values of Asp and Glu residues in staphylococcal nuclease. Proteins, vol.77, no.3, 570-588.

상세보기
Yao, Guorui, Zong, Yinong, Gu, Shenyan, Zhou, Jie, Xu, Huaxi, Mathews, Irimpan I., Jin, Rongsheng. Crystal structure of the glutamate receptor GluA1 N-terminal domain. The Biochemical journal, vol.438, no.2, 255-263.

상세보기
Coleman, Ryan G., Sharp, Kim A.. Protein Pockets: Inventory, Shape, and Comparison. Journal of chemical information and modeling, vol.50, no.4, 589-603.

상세보기
10.1109/XSW.2013.10
Chavent, Matthieu, Duncan, Anna L, Sansom, Mark SP. Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale. Current opinion in structural biology, vol.40, 8-16.

상세보기
Goh, Boon Chong, Hadden, Jodi A., Bernardi, Rafael C., Singharoy, Abhishek, McGreevy, Ryan, Rudack, Till, Cassidy, C. Keith, Schulten, Klaus. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Annual review of biophysics, vol.45, 253-278.

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