dissertation-template/biblio.bib

@article{Abraham2015,
  title = {{{GROMACS}}: {{High}} Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers},
  author = {Abraham, Mark James and Murtola, Teemu and Schulz, Roland and Páll, Szilárd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik},
  date = {2015},
  journaltitle = {SoftwareX},
  volume = {1},
  pages = {19--25},
  issn = {23527110},
  doi = {10.1016/j.softx.2015.06.001},
  abstract = {GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.},
  keywords = {\#nosource},
  file = {/home/bauer/Zotero/storage/W2EN24B4/Abraham et al_2015_GROMACS.pdf}
}

@article{Alam2009,
  title = {High-Resolution Structure of the Open {{NaK}} Channel},
  author = {Alam, Amer and Jiang, Youxing},
  date = {2009-01-21},
  journaltitle = {Nature Structural \& Molecular Biology},
  volume = {16},
  number = {1},
  pages = {30--34},
  issn = {1545-9993},
  doi = {10.1038/nsmb.1531},
  abstract = {We report the crystal structure of the nonselective cation channel NaK from Bacillus cereus at a resolution of 1.6 Å . The structure reveals the intracellular gate in an open state, as opposed to the closed form reported previously, making NaK the only channel for which the three-dimensional structures of both conformations are known. Channel opening follows a conserved mechanism of inner helix bending using a flexible glycine residue, the gating hinge, seen in MthK and most other tetrameric cation channels. Additionally, distinct inter and intrasubunit rearrangements involved in channel gating are seen and characterized for the first time along with inner helix twisting motions. Furthermore, we identify a residue deeper within the cavity of the channel pore, Phe92, which is likely to form a constriction point within the open pore, restricting ion flux through the channel. Mutating this residue to alanine causes a subsequent increase in ion-conduction rates as measured by 86 Rb flux assays. The structures of both the open and closed conformations of the NaK channel correlate well with those of equivalent K + channel conformations, namely MthK and KcsA, respectively. The opening and closing of ion channel pores in response to external stimuli such as voltage or ligand binding is a process of extreme importance to ion channel physiology 1 . Until now, our knowledge of the open and closed conformations of tetrameric cation channel pores comes predominantly from the crystal structures of various K + channels, among which the structures of KcsA and MthK have been generally accepted as reasonable models for the closed and open conformations of tetrameric cation channel pores, respectively 2–9 . The closed conformation is characterized by near-straight inner helices and the subsequent bundle crossing that is formed by interactions between their C-terminal residues. In the open conformation seen in the MthK structure, the inner helices seem to bend at a conserved glycine residue, the gating hinge also seen in most other cation channels, resulting in the disruption of the bundle crossing. However, structural information on both states from the same channel has so far been lacking. In the process of studying the ion-selectivity properties of the NaK channel, which shares overall sequence and structural similarities with KcsA, except in the selectivity filter region, and conducts both Na + and K + (refs. 10,11), we crystallized a truncated construct (NaKND19) lacking its N-terminal M0 helix and determined its structure at a resolution of 1.6 Å . Unexpectedly, the NaKND19 structure reveals the intracellular gate in an open conformation. Combined with the closed conformation structure of NaK, the new structure provides a unique opportunity to analyze in detail the structural features underlying pore opening and closing within the same channel. We observe both inner helix twisting and bending at the glycine gating hinge upon pore opening. Our data clearly demonstrate the conservation of central sequence and structural motifs involved in channel opening, while also offering insight into the intricate rearrangements of interactions within and between channel subunits upon undergoing gating transi-tions. In addition, the high-resolution structures also allow us to carry out an analysis of the molecular details of ion binding in the NaK selectivity filter, which we report in our companion paper 12 .},
  keywords = {\#nosource},
  file = {/home/bauer/Zotero/storage/L33BLVLV/Alam_Jiang_2009_High-resolution structure of the open NaK channel.pdf}
}

@article{Biggin2000,
  ids = {biggin2000},
  title = {Potassium Channel Structure: Domain by Domain},
  author = {Biggin, Phil C. and Roosild, Tarmo and Choe, Senyon},
  date = {2000-08},
  journaltitle = {Current Opinion in Structural Biology},
  volume = {10},
  number = {4},
  eprint = {10981635},
  eprinttype = {pmid},
  pages = {456--461},
  issn = {0959-440X},
  doi = {10.1016/S0959-440X(00)00114-7},
  abstract = {Since the determination of the structure of a bacterial potassium channel, the ion channel community has managed to gain momentum in the quest for a complete picture. The information is coming at a steady flow, on a domain by domain basis. Recent discoveries are starting to reveal clues to the complex manner in which potassium channels show enormous diversity of function and also to their methods of regulation. Currently, the structures of four domains are known, with the most recent addition being the Kv?? structure. As efforts continue in the study of the transmembrane domains, especially the voltage-sensing apparatus, there has been a new realization with respect to the identification and role of the cytoplasmic domains in protein-protein interactions in particular. An additional discovery, considerably aided by recent genomic analysis, is that potassium channels comprising subunits with two pore regions and four transmembrane helices combined in a dimeric fashion are abundant and are probable targets for local anesthetics.},
  isbn = {0959-440X (Print)},
  keywords = {Anesthetics,Beta subunit,BTB/POZ,Domains,KcsA,NAD,Potassium channels,Protein-protein interaction,Structure,T1},
  file = {/home/bauer/Zotero/storage/5KMKYJVX/Biggin et al_2000_Potassium channel structure.pdf;/home/bauer/Zotero/storage/KI98GGZ7/Biggin et al_2000_Potassium channel structure.pdf;/home/bauer/Zotero/storage/PG8BRYFT/S0959440X00001147.html}
}

@book{book:1314973,
  title = {Handbook of Ion Channels},
  author = {Trudeau, Matthew C. and Zheng, Jie},
  date = {2015},
  edition = {1},
  publisher = {{CRC Press}},
  isbn = {978-1-4665-5142-8 1-4665-5142-9},
  file = {/home/bauer/Zotero/storage/A2UIWBQT/Trudeau_2015_Handbook of ion channels.pdf}
}