Registro:

Referencias:

• Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., DiNola, A., Haak, J.R., Molecular dynamics with coupling to an external bath (1984) The Journal of Chemical Physics, 81 (8), p. 3684
• Blumberger, J., Lamoureux, G., Klein, M.L., Peptide hydrolysis in thermolysin: Ab initio QM/MM investigation of the Glu143-assisted water addition mechanism (2007) Journal of Chemical Theory and Computation, 3 (5), pp. 1837-1850
• Case, D.A., Babin, V., Berryman, J.T., Betz, R.M., Cai, Q., Cerutti, D.S., (2014) The Amber Molecular Dynamics Package, , http://ambermd.org/, AMBER 14 University of California San Francisco Retrieved from
• Ciulli, A., Scott, D.E., Ando, M., Reyes, F., Saldanha, S.A., Tuck, K.L., Inhibition of Mycobacterium tuberculosis pantothenate synthetase by analogues of the reaction intermediate (2008) Chembiochem: A European Journal of Chemical Biology, 9 (16), pp. 2606-2611
• Cui, Q., Elstner, M., Kaxiras, E., Frauenheim, T., Karplus, M., A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method (2001) The Journal of Physical Chemistry. B, 105 (2), pp. 569-585
• De M. Seabra, G., Walker, R.C., Elstner, M., Case, D.A., Roitberg, A.E., Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package (2007) The Journal of Physical Chemistry. A, 111 (26), pp. 5655-5664
• Ferrer, S., Ruiz-Pernía, J., Martí, S., Moliner, V., Tuñón, I., Bertrán, J., Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives (2011) Advances in Protein Chemistry and Structural Biology, 85, pp. 81-142
• Foster, M.P., Wuttke, D.S., Radhakrishnan, I., Case, D.A., Gottesfeld, J.M., Wright, P.E., Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA (1997) Nature Structural Biology, 4 (8), pp. 605-608. , http://www.ncbi.nlm.nih.gov/pubmed/9253405, Retrieved from
• Gumpena, R., Kishor, C., Ganji, R.J., Addlagatta, A., Discovery of α, β- And α, γ-diamino acid scaffolds for the inhibition of M1 family aminopeptidases (2011) ChemMedChem, 6 (11), pp. 1971-1976
• Hénin, J., Chipot, C., Overcoming free energy barriers using unconstrained molecular dynamics simulations (2004) The Journal of Chemical Physics, 121 (7), pp. 2904-2914
• Hernick, M., Fierke, C.A., Zinc hydrolases: The mechanisms of zinc-dependent deacetylases (2005) Archives of Biochemistry and Biophysics, 433 (1), pp. 71-84
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., Simmerling, C., Comparison of multiple Amber force fields and development of improved protein backbone parameters (2006) Proteins, 65 (3), pp. 712-725
• Huang, X., Hernick, M., Examination of mechanism of N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside deacetylase (MshB) reveals unexpected role for dynamic tyrosine (2012) The Journal of Biological Chemistry, 287 (13), pp. 10424-10434
• Huang, X., Kocabas, E., Hernick, M., The activity and cofactor preferences of N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase (MshB) change depending on environmental conditions (2011) The Journal of Biological Chemistry, 286 (23), pp. 20275-20282
• Jarzynski, C., Nonequilibrium equality for free energy differences (1997) Physical Review Letters, 78 (14), pp. 2690-2693
• Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L., Comparison of simple potential functions for simulating liquid water (1983) The Journal of Chemical Physics, 79 (2), p. 926
• Kamerlin, S.C.L., Warshel, A., At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? (2010) Proteins, 78 (6), pp. 1339-1375
• Koul, A., Arnoult, E., Lounis, N., Guillemont, J., Andries, K., The challenge of new drug discovery for tuberculosis (2011) Nature, 469 (7331), pp. 483-490
• Kumar, A., Kumar, S., Kumar, D., Mishra, A., Dewangan, R.P., Shrivastava, P., The structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis (2013) Acta Crystallographica. Section D, Biological Crystallography, 69, pp. 2543-2554
• Laio, A., Parrinello, M., Escaping free-energy minima (2002) Proceedings of the National Academy of Sciences of the United States of America, 99 (20), pp. 12562-12566
• Leach, A.R., (2001) Molecular Modelling: Principles and Applications, , 2nd ed. Pearson Dorset Press, Dorchester, England
• Liphardt, J., Dumont, S., Smith, S.B., Tinoco, I., Bustamante, C., Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality (2002) Science (New York, N.Y.), 296 (5574), pp. 1832-1835
• Masuyer, G., Schwager, S.L.U., Sturrock, E.D., Isaac, R.E., Acharya, K.R., Molecular recognition and regulation of human angiotensin-I converting enzyme (ACE) activity by natural inhibitory peptides (2012) Scientific Reports, 2, p. 717
• Maynes, J.T., Garen, C., Cherney, M.M., Newton, G., Arad, D., Av-Gay, Y., The crystal structure of 1-D-myo-inosityl 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase (MshB) from Mycobacterium tuberculosis reveals a zinc hydrolase with a lactate dehydrogenase fold (2003) The Journal of Biological Chemistry, 278 (47), pp. 47166-47170
• Mossessova, E., Bickford, L.C., Goldberg, J., SNARE selectivity of the COPII coat (2003) Cell, 114 (4), pp. 483-495. , http://www.ncbi.nlm.nih.gov/pubmed/12941276, Retrieved from
• Newton, G.L., Av-Gay, Y., Fahey, R.C., N-Acetyl-1-D-myo-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase (MshB) is a key enzyme in mycothiol biosynthesis (2000) Journal of Bacteriology, 182 (24), pp. 6958-6963. , http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=94821&tool=pmcentrez&rendertype=abstract, Retrieved from
• Newton, G.L., Buchmeier, N., Fahey, R.C., Biosynthesis and functions of mycothiol, the unique protective thiol of Actinobacteria (2008) Microbiology and Molecular Biology Reviews: MMBR, 72 (3), pp. 471-494
• Park, S., Khalili-Araghi, F., Tajkhorshid, E., Schulten, K., Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality (2003) The Journal of Chemical Physics, 119 (6), p. 3559
• Pohorille, A., Jarzynski, C., Chipot, C., Good practices in free-energy calculations (2010) The Journal of Physical Chemistry. B, 114 (32), pp. 10235-10253
• Prigozhin, D.M., Mavrici, D., Huizar, J.P., Vansell, H.J., Alber, T., Structural and biochemical analyses of Mycobacterium tuberculosis N-acetylmuramyl-L-alanine amidase Rv3717 point to a role in peptidoglycan fragment recycling (2013) The Journal of Biological Chemistry, 288 (44), pp. 31549-31555
• Ramírez, C.L., Zeida, A., Jara, G.E., Roitberg, A.E., Martí, M.A., Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm (2014) Journal of Chemical Theory and Computation, 10 (10), pp. 4609-4617
• Smith, C.R., Smith, G.K., Yang, Z., Xu, D., Guo, H., Quantum mechanical/molecular mechanical study of anthrax lethal factor catalysis (2010) Theoretical Chemistry Accounts, 128 (1), pp. 83-90
• Tykvart, J., Schimer, J., Bařinková, J., Pachl, P., Poštová-Slavětínská, L., Majer, P., Rational design of urea-based glutamate carboxypeptidase II (GCPII) inhibitors as versatile tools for specific drug targeting and delivery (2014) Bioorganic & Medicinal Chemistry, 22 (15), pp. 4099-4108
• Van Der Kamp, M.W., Mulholland, A.J., Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology (2013) Biochemistry, 52 (16), pp. 2708-2728
• Warshel, A., Levitt, M., Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme (1976) Journal of Molecular Biology, 103 (2), pp. 227-249
• Wilder, P.T., Varney, K.M., Weiss, M.B., Gitti, R.K., Weber, D.J., Solution structure of zinc- and calcium-bound rat S100B as determined by nuclear magnetic resonance spectroscopy (2005) Biochemistry, 44 (15), pp. 5690-5702
• Woo, T.K., Margl, P., Blöchl, P.E., Ziegler, T., Sampling phase space by a combined QM/MM ab initio Car-Parrinello molecular dynamics method with different (multiple) time steps in the quantum mechanical (QM) and molecular mechanical (MM) domains (2002) The Journal of Physical Chemistry. A, 106 (7), pp. 1173-1182
• Wyckoff, T.J., Taylor, J.A., Salama, N.R., Beyond growth: Novel functions for bacterial cell wall hydrolases (2012) Trends in Microbiology, 20 (11), pp. 540-547
• Xiong, H., Crespo, A., Marti, M., Estrin, D., Roitberg, A.E., Free energy calculations with non-equilibrium methods: Applications of the Jarzynski relationship (2006) Theoretical Chemistry Accounts, 116 (1-3), pp. 338-346
• Xu, D., Guo, H., Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism (2009) Journal of the American Chemical Society, 131 (28), pp. 9780-9788
• Yang, Y., Liu, C., Lin, Y.-L., Li, F., Structural insights into central hypertension regulation by human aminopeptidase A (2013) The Journal of Biological Chemistry, 288 (35), pp. 25638-25645
• Zhang, C., Wu, S., Xu, D., Catalytic mechanism of angiotensin-converting enzyme and effects of the chloride ion (2013) The Journal of Physical Chemistry. B, 117 (22), pp. 6635-6645
• Zheng, L., Chen, M., Yang, W., Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems (2008) Proceedings of the National Academy of Sciences of the United States of America, 105 (51), pp. 20227-20232
• Zimmermann, M., Clarke, O., Gulbis, J.M., Keizer, D.W., Jarvis, R.S., Cobbett, C.S., Metal binding affinities of Arabidopsis zinc and copper transporters: Selectivities match the relative, but not the absolute, affinities of their amino-terminal domains (2009) Biochemistry, 48 (49), pp. 11640-11654A4 -

Citas:

---------- APA ----------

---------- CHICAGO ----------

---------- MLA ----------

---------- VANCOUVER ----------