Seminarium do wykładu: Modelowanie molekularne II

Lista artykułów z zastosowań modelowania molekularnego w badaniach bioukładów do wyboru w roku akad. 2017/2018

Proszę zachować zadaną kolejność referowania

10. How computational models can help unlock biological systems. G. W. Brodland. Seminars in Cell & Developmental Biology. 2015;

1. Water? What’s so special about it? J. L. Finney. Phil. Trans. R. Soc. Lond. B 359, 1145–1165, 2004. (do zreferowania są następujące sekcje: 1, 2, 3, 4f, 5, 6).

2. The Grotthuss mechanism. N. Agmon. Chemical Physics Letters. 244, 456-462, 1995.

3. Water conduction through the hydrophobic channel of a carbon nanotube G. Hummer, J. C. Rasaiah and J. P. Noworyta. Nature. 414, 188-190, 2001. (3-4 referuje jedna osoba)

4. Water at the nanoscale. M. S. P. Sansom and Ph. C. Biggin. Nature. 414, 156-158, 2001. (3-4 referuje jedna osoba)

5. Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation. A. C. Fogarty and D. Laage. J. Phys. Chem. B 118, 7715−7729, 2014.

6. Molecular dynamics simulation for the structure of the water chain in a transmembrane peptide nanotube. J. Liu et al., J. Phys. Chem. A 114, 2376-2383, 2010. <<br>>

7. Single-channel permeability and glycerol affinity of human aquaglyceroporin AQP3. R. A. Rodriguez et al. Biochim. Biophys. Acta- Biomembranes 1861, 768–775, 2019 + SI

8. The Mechanism of Na+/K+ selectivity in mammalian voltage-gated sodium channels based on molecular dynamics simulation. M. Xia et al. Biophys. J. 104 , 2401-2409, 2013 + Supplem.

9. Current progress in structure-based rational drug design marks a new mindset in drug discovery. V. Lounnas et al. Comp. Struct. Biotechnol. J. 5, e201302011, 2013.

10. A whole-cell computational model predicts phenotype from genotype. J. R. Karr et al. Cell. 150, 389-401, 2012.

Artykuły do wyboru

8. a-Helical structures drive early stages of self-assembly of amyloidogenic amyloid polypeptide aggregate formation in membranes. M. Pannuzzo, A. Raudino, D. Milardi, C. La Rosa and M. Karttunen.Scientific Reports 3 :2781, 1-10, 2013.

9. Atomistic molecular-dynamics simulations enable prediction of the arginine permeation pathway through OccD1/OprD from ''Pseudomonas aeruginosa''. J. Parkin and S. Khalid. Biophys. J. 107, 1853–1861, 2014.

10. Time-resolved cryo-electron microscopy: Recent progress. Joachim Frank. J. Struc. Biol., 2017,

11. Protein folding at extreme temperatures: Current issue. Georges Feller. Seminars in Cell & Developmental Biology, 2017,

12. Fractal properties of cell surface structures: A view from AFM. A. Bitler, R. S. Dover, Y. Shai. Seminars in Cell & Developmental Biology, 2017,

Strong preferences of dopamine and l-dopa towards lipid head group: importance of lipid composition and implication for neurotransmitter metabolism. A. Orłowski, M. Grzybek, A. Bunker, M. Pasenkiewicz-Gierula, I. Vattulainen, P. T. Männistö and T. Róg. J. Neurochemistry, 122, 681–690, 2012.

13. Water isotope effect on the phosphatidylcholine bilayer properties: a molecular dynamics simulation study. T. Róg, K. Murzyn, J. Milhaud, M. Karttunen and M. Pasenkiewicz-Gierula. Phys. Chem. B 113, 2378-2387, 2009.

14. Water–protein interactions from high-resolution protein crystallography. M. Nakasako. Phil. Trans. R. Soc. London. B. 359, 1191-1206, 2004.

Lista artykułów z metodologii badań bioukładów molekularnych do wyboru w roku akad. 2017/2018

  1. Atomic-level characterization of the structural dynamics of proteins. David E. Shaw, et al., Science 330, 341-346, 2010.

  2. Regulation of the protein-conducting channel by a bound ribosome. J. Gumbart, L. G. Trabuco, E. Schreiner, E. Villa, K. Schulten. Structure 17, 1453–1464, 2009.

  3. Common structural transitions in explicit-solvent simulations of villin headpiece folding. P. L. Freddolino, K. Schulten. Bioph. J. 97, 2338–2347, 2009.

  4. Unusual biophysics of intrinsically disordered proteins. V. N. Uversky. Biochim. Biophys. Acta 1834, 932–951, 2013.

  5. Do all backbone polar groups in proteins form hydrogen bonds? P. J. Fleming and G. D. Rose. Protein Science, 14, 1911–1917, 2005.

  6. The Levinthal paradox of the interactome. P. Tompa and G. D. Rose. Protein Science, 20, 2074-2079, 2011. lub (6 lub 7)

  7. Levinthal’s paradox revisited, and dismissed. A. Ben-Naim. Open Journal of Biophysics, 2, 23-32, 2012.

  8. Membrane binding of recoverin: from mechanistic understanding to biological functionality. Š. Timr, R. Pleskot, J. Kadlec, M. Kohagen, A. Magarkar, and P. Jungwirth. ACS Central Science, 3, 868−874, 2017 + SI – referują 2 osoby

  9. How to minimize artifacts in atomistic simulations of membrane proteins, whose crystal structure is heavily engineered: β2‑adrenergic receptor in the spotlight. M. Manna, W. Kulig, M. Javanainen, J. Tynkkynen, U. Hensen, D. J. Müller, T. Rog, and I. Vattulainen. Journal of Chemical Theory and Computation 11, 3432–3445, 2015 + SI– referują 2 osoby.

  10. Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides. M. B. Ulmschneider, J. P. F. Doux, J. A. Killian, J. C. Smith, and J. P. Ulmschneider. J. Am. Chem. Soc. 132, 3452–3460, 2010.

  11. Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots. M. Sikora, J. I. Sułkowska, M. Cieplak.

  12. Normal Modes and Essential Dynamics. in: Methods in molecular biology, S. Hayward and B. L. de Groot. vol 443, Molecular modelling of proteins 89-106, 2008.

BioInfoCourses: ModMol2/Seminars (last edited 2020-11-25 13:58:50 by MartaPasenkiewiczGierula)