wepy.lysozyme_test/project.bib

@article{Baase2010T4LysozymeReview,
abstract = {An overview is presented of some of the major insights that have come from studies of the structure, stability, and folding of T4 phage lysozyme. A major purpose of this review is to provide the reader with a complete tabulation of all of the variants that have been characterized, including melting temperatures, crystallographic data, Protein Data Bank access codes, and references to the original literature. The greatest increase in melting temperature (T(m)) for any point mutant is 5.1 degrees C for the mutant Ser 117 --> Val. This is achieved in part not only by hydrophobic stabilization but also by eliminating an unusually short hydrogen bond of 2.48 A that apparently has an unfavorable van der Waals contact. Increases in T(m) of more than 3-4 degrees C for point mutants are rare, whereas several different types of destabilizing substitutions decrease T(m) by 20 degrees C or thereabouts. The energetic cost of cavity creation and its relation to the hydrophobic effect, derived from early studies of "large-to-small" mutants in the core of T4 lysozyme, has recently been strongly supported by related studies of the intrinsic membrane protein bacteriorhodopsin. The L99A cavity in the C-terminal domain of the protein, which readily binds benzene and many other ligands, has been the subject of extensive study. Crystallographic evidence, together with recent NMR analysis, suggest that these ligands are admitted by a conformational change involving Helix F and its neighbors. A total of 43 nonisomorphous crystal forms of different monomeric lysozyme mutants were obtained plus three more for synthetically-engineered dimers. Among the 43 space groups, P2(1)2(1)2(1) and P2(1) were observed most frequently, consistent with the prediction of Wukovitz and Yeates.},
author = {Baase, W A and Liu, L and Tronrud, D E and Matthews, B W},
journal = {Protein Sci},
misc = {  pmid = {20095051},
  doi = {10.1002/pro.344}},
month = {apr},
number = {4},
pages = {631-641},
title = {Lessons from the lysozyme of phage T4},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867005/},
volume = {19},
year = {2010}
}



@article{NunesAlves2018T4LysozymeUnbinding,
abstract = {The T4 lysozyme L99A mutant is often used as a model system to study small-molecule binding to proteins, but pathways for ligand entry and exit from the buried binding site and the associated protein conformational changes have not been fully resolved. Here, molecular dynamics simulations were employed to model benzene exit from its binding cavity using the weighted ensemble (WE) approach to enhance sampling of low-probability unbinding trajectories. Independent WE simulations revealed four pathways for benzene exit, which correspond to transient tunnels spontaneously formed in previous simulations of apo T4 lysozyme. Thus, benzene unbinding occurs through multiple pathways partially created by intrinsic protein structural fluctuations. Motions of several α-helices and side chains were involved in ligand escape from metastable microstates. WE simulations also provided preliminary estimates of rate constants for each exit pathway. These results complement previous works and provide a semiquantitative characterization of pathway heterogeneity for binding of small molecules to proteins.},
author = {Nunes-Alves, Ariane and Zuckerman, Daniel M. and Arantes, Guilherme Menegon},
journal = {Biophysical Journal},
misc = {  issn = {0006-3495},
  doi = {https://doi.org/10.1016/j.bpj.2018.01.014}},
number = {5},
pages = {1058 - 1066},
title = {Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways},
url = {http://www.sciencedirect.com/science/article/pii/S0006349518301401},
volume = {114},
year = {2018}
}



@article{Wang2016LysozymeMetadynamicsUnbinding,
author = {Wang, Yong and Papaleo, Elena and Lindorff-Larsen, Kresten},
journal = {Elife},
pages = {e17505},
publisher = {eLife Sciences Publications Limited},
title = {Mapping transiently formed and sparsely populated conformations on a complex energy landscape},
volume = {5},
year = {2016}
}



@article{Feher1996LysozymeBinding,
author = {Feher, Victoria A and Baldwin, Enoch P and Dahlquist, Frederick W},
journal = {Nature structural biology},
number = {6},
pages = {516},
publisher = {Nature Publishing Group},
title = {Access of ligands to cavities within the core of a protein is rapid},
volume = {3},
year = {1996}
}