@string{EABayer = "Bayer, Edward A."}
@string{EBeasley = "Beasley, E."}
@string{JBechhoefer = "Bechhoefer, John"}
+@string{BBechinger = "Bechinger, Burkhard"}
@string{ABecker = "Becker, Anke"}
@string{GSBeddard = "Beddard, Godfrey S."}
@string{TBeebe = "Beebe, Thomas P."}
@string{EChapman = "Chapman, Edwin R."}
@string{RCharlab = "Charlab, R."}
@string{KChaturvedi = "Chaturvedi, K."}
+@string{AChauhan = "Chauhan, A."}
+@string{VPChauhan = "Chauhan, V.~P."}
@string{CChauzy = "Chauzy, C."}
@string{SChe = "Che, Shunai"}
@string{CEC = "Chemical Engineering Communications"}
@string{MCoyne = "Coyne, M."}
@string{DCraig = "Craig, David"}
@string{ACravchik = "Cravchik, A."}
+@string{PSCremer = "Cremer, Paul S."}
@string{CCroarkin = "Croarkin, Carroll"}
@string{VCroquette = "Croquette, Vincent"}
@string{YCui = "Cui, Y."}
@string{COSB = "Current Opinion in Structural Biology"}
+@string{COCB = "Current Opinion in Chemical Biology"}
@string{LCurry = "Curry, L."}
@string{CDahlke = "Dahlke, C."}
@string{FDahlquist = "Dahlquist, Frederick W."}
@string{TDrobek = "Drobek, T."}
@string{Drexel = "Drexel University"}
@string{OKDudko = "Dudko, Olga K."}
+@string{YFDufrene = "Dufr{\^e}ne, Yves F."}
@string{ADunham = "Dunham, A."}
@string{DDunlap = "Dunlap, D."}
@string{PDunn = "Dunn, P."}
+@string{VDupres = "Dupres, Vincent"}
@string{EMBORep = "EMBO Rep"}
@string{EMBO = "EMBO Rep."}
@string{REckel = "Eckel, R."}
@string{LFrench = "French, L."}
@string{RWFriddle = "Friddle, Raymond W."}
@string{CFriedman = "Friedman, C."}
+@string{RFriedman = "Friedman, Ran"}
@string{MFritz = "Fritz, M."}
@string{HFuchs = "Fuchs, Harald"}
@string{TFujii = "Fujii, Tadashi"}
@string{HJGuntherodt = "Guntherodt, Hans-Joachim"}
@string{NGuo = "Guo, N."}
@string{YGuo = "Guo, Yi"}
+@string{MGutman = "Gutman, Menachem"}
@string{RTGuy = "Guy, Richard T."}
@string{PHanggi = {H\"anggi, Peter}}
@string{THa = "Ha, Taekjip"}
@string{TInoue = "Inoue, Tadashi"}
@string{IJBMM = "International Journal of Biological Macromolecules"}
@string{IJCIS = "International Journal of Computer \& Information Sciences"}
+@string{AItkin = "Itkin, Anna"}
@string{HItoh = "Itoh, Hiroyasu"}
@string{AIrback = "Irback, Anders"}
+@string{AMIsaacs = "Isaacs, Adrian M."}
@string{BIsralewitz = "Isralewitz, B."}
@string{SIstrail = "Istrail, S."}
@string{MIvemeyer = "Ivemeyer, M."}
@string{KAPPP = "Kluwer Academic Publishers--Plenum Publishers"}
@string{CDKodira = "Kodira, C. D."}
@string{SKoduru = "Koduru, S."}
+@string{PKoehl = "Koehl, Patrice"}
@string{BKolmerer = "Kolmerer, B."}
@string{JKorenberg = "Korenberg, J."}
@string{IKosztin = "Kosztin, Ioan"}
@string{CCMello = "Mello, Cecilia C."}
@string{RMerkel = "Merkel, R."}
@string{GVMerkulov = "Merkulov, G. V."}
+@string{FMerzel = "Merzel, Franci"}
@string{HMetiu = "Metiu, Horia"}
@string{NMetropolis = "Metropolis, Nicholas"}
@string{GMeyer = "Meyer, Gerhard"}
@string{HMi = "Mi, H."}
+@string{LMiao = "Miao, Linlin"}
@string{CMicheletti = "Micheletti, Cristian"}
@string{MMickler = "Mickler, Moritz"}
@string{AMiller = "Miller, A."}
@string{EWMyers = "Myers, E. W."}
@string{RMMyers = "Myers, R. M."}
@string{AMylonakis = "Mylonakis, Andreas"}
+@string{ENachliel = "Nachliel, Esther"}
@string{JNadeau = "Nadeau, J."}
@string{AKNaik = "Naik, A. K."}
@string{NANO = "Nano letters"}
@string{CNelson = "Nelson, C."}
@string{KNelson = "Nelson, K."}
@string{RRNetz = "Netz, R.~R."}
+@string{NR = "Neurochemical research"}
@string{NEURON = "Neuron"}
@string{RNevo = "Nevo, Reinat"}
@string{NJP = "New Journal of Physics"}
@string{GPing = "Ping, Guanghui"}
@string{NPinotsis = "Pinotsis, Nikos"}
@string{MPlumbley = "Plumbley, Mark"}
+@string{PLOS:ONE = "PLOS ONE"}
+%string{PLOS:ONE = "Public Library of Science ONE"}
@string{DPlunkett = "Plunkett, David"}
@string{PPodsiadlo = "Podsiadlo, Paul"}
@string{ASPolitou = "Politou, A. S."}
@string{EPuchner = "Puchner, Elias M."}
@string{VPuri = "Puri, V."}
@string{WPyckhout-Hintzen = "Pyckhout-Hintzen, Wim"}
+@string{HQin = "Qin, Haina"}
@string{SQin = "Qin, S."}
@string{SRQuake = "Quake, Stephen R."}
@string{CQuate = "Quate, Calvin F."}
@string{LRamirez = "Ramirez, L."}
@string{JRamser = "Ramser, J."}
@string{LRandles = "Randles, Lucy G."}
+@string{VRaussens = "Raussens, Vincent"}
+@string{IRay = "Ray, I."}
@string{MReardon = "Reardon, M."}
@string{ALCReddin = "Reddin, Andrew L. C."}
@string{SRedick = "Redick, Sambra D."}
@string{LRowen = "Rowen, L."}
@string{BRuhfel = "Ruhfel, B."}
@string{DBRusch = "Rusch, D. B."}
+@string{JMRuysschaert = "Ruysschaert, Jean-Marie"}
@string{JPRyckaert = "Ryckaert, Jean-Paul"}
@string{NSakaki = "Sakaki, Naoyoshi"}
@string{YSakaki = "Sakaki, Y."}
@string{MSekhon = "Sekhon, M."}
@string{TSekiguchi = "Sekiguchi, T."}
@string{BSenger = "Senger, B."}
+@string{DBSenn = "Senn, David B."}
@string{PSeranski = "Seranski, P."}
@string{RSesboue = {Sesbo\"u\'e, R.}}
@string{EShakhnovich = "Shakhnovich, Eugene"}
@string{AShimizu = "Shimizu, A."}
@string{NShimizu = "Shimizu, N."}
@string{RShimoKon = "Shimo-Kon, Rieko"}
+@string{JPShine = "Shine, James P."}
@string{AShintani = "Shintani, A."}
@string{BShneiderman = "Shneiderman, Ben"}
@string{BShue = "Shue, B."}
@string{SEG = "Society of Exploration Geophysicists"}
@string{ESodergren = "Sodergren, E."}
@string{CSoderlund = "Soderlund, C."}
+@string{JSong = "Song, Jianxing"}
@string{JSpanier = "Spanier, Jonathan E."}
@string{DSpeicher = "Speicher, David W."}
@string{GSpier = "Spier, G."}
@string{SJBTendler = "Tendler, S.~J.~B."}
@string{STeukolsky = "Teukolsky, S."}
@string{CJ = "The Computer Journal"}
+@string{JBC = "The Journal of Biological Chemistry"}
@string{JCP = "The Journal of Chemical Physics"}
@string{JPC:B = "The Journal of Physical Chemistry B"}
@string{JPC:C = "The Journal of Physical Chemistry C"}
@string{KWatanabe = "Watanabe, Kaori"}
@string{RHWaterston = "Waterston, R. H."}
@string{BWaugh = "Waugh, Ben"}
+@string{JWegiel = "Wegiel, J."}
@string{MWei = "Wei, M."}
@string{YWei = "Wei, Yen"}
@string{ALWeisenhorn = "Weisenhorn, A.~L."}
@string{SWindsor = "Windsor, S."}
@string{EWinn-Deen = "Winn-Deen, E."}
@string{NWirth = "Wirth, Niklaus"}
+@string{HMWisniewski = "Wisniewski, H.~M."}
@string{CWitt = "Witt, Christian"}
@string{KWolfe = "Wolfe, K."}
@string{TGWolfsberg = "Wolfsberg, T. G."}
@string{MYandell = "Yandell, M."}
@string{GYang = "Yang, Guoliang"}
@string{YYang = "Yang, Yao"}
+@string{BAYankner = "Yankner, Bruce A."}
@string{AYao = "Yao, A."}
@string{RYasuda = "Yaduso, Ryohei"}
@string{JYe = "Ye, J."}
@string{MYoshida = "Yoshida, Masasuke"}
@string{WYu = "Yu, Weichang"}
@string{JMYuan = "Yuan, Jian-Min"}
+@string{MYuan = "Yuan, Menglan"}
@string{AZandieh = "Zandieh, A."}
@string{JZaveri = "Zaveri, J."}
@string{KZaveri = "Zaveri, K."}
@string{JZhang = "Zhang, J."}
@string{QZhang = "Zhang, Q."}
@string{WZhang = "Zhang, W."}
+@string{YZhang = "Zhang, Yanjie"}
@string{ZZhang = "Zhang, Zongtao"}
@string{JZhao = "Zhao, Jason Ming"}
@string{LZhao = "Zhao, Liming"}
@string{XZhu = "Zhu, X."}
@string{YJZhu = "Zhu, Ying-Jie"}
@string{WZhuang = "Zhuang, Wei"}
+@string{JZidar = "Zidar, Jernej"}
@string{JZiegler = "Ziegler, J.G."}
@string{NZinder = "Zinder, N."}
@string{RCZinober = "Zinober, Rebecca C."}
note = {Higher resolution pictures are available at
\url{http://antlab.gatech.edu/antlab/The_Ant_Raft.html}.},
}
+
+@article{ chauhan97,
+ author = VPChauhan #" and "# IRay #" and "# AChauhan #" and "#
+ JWegiel #" and "# HMWisniewski,
+ title = {Metal cations defibrillize the amyloid beta-protein fibrils.},
+ year = 1997,
+ month = jul,
+ address = {New York State Institute for Basic Research in
+ Developmental Disabilities, Staten Island 10314-6399,
+ USA.},
+ journal = NR,
+ volume = 22,
+ number = 7,
+ pages = {805--809},
+ issn = {0364-3190},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/9232632},
+ language = {eng},
+ keywords = {Alzheimer Disease},
+ keywords = {Amyloid beta-Peptides},
+ keywords = {Drug Evaluation, Preclinical},
+ keywords = {Humans},
+ keywords = {Metals},
+ keywords = {Peptide Fragments},
+ keywords = {Solubility},
+ abstract = {Amyloid beta-protein (A beta) is the major constituent
+ of amyloid fibrils composing beta-amyloid plaques and
+ cerebrovascular amyloid in Alzheimer's disease (AD). We studied
+ the effect of metal cations on preformed fibrils of synthetic A
+ beta by Thioflavin T (ThT) fluorescence spectroscopy and
+ electronmicroscopy (EM) in negative staining. The amount of cross
+ beta-pleated sheet structure of A beta 1-40 fibrils was found to
+ decrease by metal cations in a concentration-dependent manner as
+ measured by ThT fluorescence spectroscopy. The order of
+ defibrillization of A beta 1-40 fibrils by metal cations was: Ca2+
+ and Zn2+ (IC50 = 100 microM) > Mg3+ (IC50 = 300 microM) > Al3+
+ (IC50 = 1.1 mM). EM analysis in negative staining showed that A
+ beta 1-40 fibrils in the absence of cations were organized in a
+ fine network with a little or no amorphous material. The addition
+ of Ca2+, Mg2+, and Zn2+ to preformed A beta 1-40 fibrils
+ defibrillized the fibrils or converted them into short rods or to
+ amorphous material. Al3+ was less effective, and reduced the
+ fibril network by about 80\% of that in the absence of any metal
+ cation. Studies with A beta 1-42 showed that this peptide forms
+ more dense network of fibrils as compared to A beta 1-40. Both ThT
+ fluorescence spectroscopy and EM showed that similar to A beta
+ 1-40, A beta 1-42 fibrils are also defibrillized in the presence
+ of millimolar concentrations of Ca2+. These studies suggest that
+ metal cations can defibrillize the fibrils of synthetic A beta.},
+}
+
+@article{ friedman05,
+ author = RFriedman #" and "# ENachliel #" and "# MGutman,
+ title = {Molecular dynamics of a protein surface: ion-residues
+ interactions.},
+ year = 2005,
+ month = aug,
+ day = 13,
+ address = {Laser Laboratory for Fast Reactions in Biology,
+ Department of Biochemistry, The George S. Wise Faculty
+ for Life Sciences, Tel Aviv University, Israel.},
+ journal = BPJ,
+ volume = 89,
+ number = 2,
+ pages = {768--781},
+ issn = {0006-3495},
+ doi = {10.1529/biophysj.105.058917},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/15894639},
+ language = {eng},
+ keywords = {Amino Acids},
+ keywords = {Binding Sites},
+ keywords = {Chlorine},
+ keywords = {Computer Simulation},
+ keywords = {Ions},
+ keywords = {Models, Chemical},
+ keywords = {Models, Molecular},
+ keywords = {Motion},
+ keywords = {Protein Binding},
+ keywords = {Protein Conformation},
+ keywords = {Ribosomal Protein S6},
+ keywords = {Sodium},
+ keywords = {Solutions},
+ keywords = {Static Electricity},
+ keywords = {Surface Properties},
+ keywords = {Water},
+ abstract = {Time-resolved measurements indicated that protons could
+ propagate on the surface of a protein or a membrane by a special
+ mechanism that enhanced the shuttle of the proton toward a
+ specific site. It was proposed that a suitable location of
+ residues on the surface contributes to the proton shuttling
+ function. In this study, this notion was further investigated by
+ the use of molecular dynamics simulations, where Na(+) and Cl(-)
+ are the ions under study, thus avoiding the necessity for quantum
+ mechanical calculations. Molecular dynamics simulations were
+ carried out using as a model a few Na(+) and Cl(-) ions enclosed
+ in a fully hydrated simulation box with a small globular protein
+ (the S6 of the bacterial ribosome). Three independent 10-ns-long
+ simulations indicated that the ions and the protein's surface were
+ in equilibrium, with rapid passage of the ions between the
+ protein's surface and the bulk. However, it was noted that close
+ to some domains the ions extended their duration near the surface,
+ thus suggesting that the local electrostatic potential hindered
+ their diffusion to the bulk. During the time frame in which the
+ ions were detained next to the surface, they could rapidly shuttle
+ between various attractor sites located under the electrostatic
+ umbrella. Statistical analysis of the molecular dynamics and
+ electrostatic potential/entropy consideration indicated that the
+ detainment state is an energetic compromise between attractive
+ forces and entropy of dilution. The similarity between the motion
+ of free ions next to a protein and the proton transfer on the
+ protein's surface are discussed.},
+}
+
+@article{ friedman11,
+ author = RFriedman,
+ title = {Ions and the protein surface revisited: extensive molecular
+ dynamics simulations and analysis of protein structures in
+ alkali-chloride solutions.},
+ year = 2011,
+ month = jul,
+ day = 28,
+ address = {School of Natural Sciences, Linn{\ae}us University,
+ 391 82 Kalmar, Sweden. ran.friedman@lnu.se},
+ journal = JPC:B,
+ volume = 115,
+ number = 29,
+ pages = {9213--9223},
+ issn = {1520-5207},
+ doi = {10.1021/jp112155m},
+ URL = {http://www.ncbi.nlm.nih.gov/pubmed/21688775},
+ language = {eng},
+ keywords = {Alkalies},
+ keywords = {Amyloid},
+ keywords = {Chlorides},
+ keywords = {Databases, Protein},
+ keywords = {Fungal Proteins},
+ keywords = {HIV Protease},
+ keywords = {Humans},
+ keywords = {Molecular Dynamics Simulation},
+ keywords = {Protein Multimerization},
+ keywords = {Protein Structure, Secondary},
+ keywords = {Proteins},
+ keywords = {Ribosomal Protein S6},
+ keywords = {Solutions},
+ keywords = {Solvents},
+ keywords = {Surface Properties},
+ abstract = {Proteins interact with ions in various ways. The surface
+ of proteins has an innate capability to bind ions, and it is also
+ influenced by the screening of the electrostatic potential owing
+ to the presence of salts in the bulk solution. Alkali metal ions
+ and chlorides interact with the protein surface, but such
+ interactions are relatively weak and often transient. In this
+ paper, computer simulations and analysis of protein structures are
+ used to characterize the interactions between ions and the protein
+ surface. The results show that the ion-binding properties of
+ protein residues are highly variable. For example, alkali metal
+ ions are more often associated with aspartate residues than with
+ glutamates, whereas chlorides are most likely to be located near
+ arginines. When comparing NaCl and KCl solutions, it was found
+ that certain surface residues attract the anion more strongly in
+ NaCl. This study demonstrates that protein-salt interactions
+ should be accounted for in the planning and execution of
+ experiments and simulations involving proteins, particularly if
+ subtle structural details are sought after.},
+}
+
+@article{ zhang06,
+ author = YZhang #" and "# PSCremer,
+ title = {Interactions between macromolecules and ions: The
+ {H}ofmeister series.},
+ year = 2006,
+ month = dec,
+ day = 10,
+ address = {Department of Chemistry, Texas A\&M University,
+ College Station, TX 77843, USA.},
+ journal = COCB,
+ volume = 10,
+ number = 6,
+ pages = {658--663},
+ issn = {1367-5931},
+ doi = {10.1016/j.cbpa.2006.09.020},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/17035073},
+ language = {eng},
+ keywords = {Acrylamides},
+ keywords = {Biopolymers},
+ keywords = {Solubility},
+ keywords = {Thermodynamics},
+ keywords = {Water},
+ abstract = {The Hofmeister series, first noted in 1888, ranks the
+ relative influence of ions on the physical behavior of a wide
+ variety of aqueous processes ranging from colloidal assembly to
+ protein folding. Originally, it was thought that an ion's
+ influence on macromolecular properties was caused at least in part
+ by `making' or `breaking' bulk water structure. Recent
+ time-resolved and thermodynamic studies of water molecules in salt
+ solutions, however, demonstrate that bulk water structure is not
+ central to the Hofmeister effect. Instead, models are being
+ developed that depend upon direct ion-macromolecule interactions
+ as well as interactions with water molecules in the first
+ hydration shell of the macromolecule.},
+}
+
+@article{ isaacs06,
+ author = AMIsaacs #" and "# DBSenn #" and "# MYuan #" and "#
+ JPShine #" and "# BAYankner,
+ title = {Acceleration of amyloid beta-peptide aggregation by
+ physiological concentrations of calcium.},
+ year = 2006,
+ month = sep,
+ day = 22,
+ address = {Department of Neurology and Division of Neuroscience,
+ The Children's Hospital, Harvard Medical School,
+ Boston, Massachusetts 02115, USA.},
+ journal = JBC,
+ volume = 281,
+ number = 38,
+ pages = {27916--27923},
+ issn = {0021-9258},
+ doi = {10.1074/jbc.M602061200},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/16870617},
+ language = {eng},
+ keywords = {Alzheimer Disease},
+ keywords = {Amyloid},
+ keywords = {Amyloid beta-Peptides},
+ keywords = {Animals},
+ keywords = {Calcium},
+ keywords = {Cells, Cultured},
+ keywords = {Copper},
+ keywords = {Neurons},
+ keywords = {Rats},
+ keywords = {Zinc},
+ abstract = {Alzheimer disease is characterized by the accumulation
+ of aggregated amyloid beta-peptide (Abeta) in the brain. The
+ physiological mechanisms and factors that predispose to Abeta
+ aggregation and deposition are not well understood. In this
+ report, we show that calcium can predispose to Abeta aggregation
+ and fibril formation. Calcium increased the aggregation of early
+ forming protofibrillar structures and markedly increased
+ conversion of protofibrils to mature amyloid fibrils. This
+ occurred at levels 20-fold below the calcium concentration in the
+ extracellular space of the brain, the site at which amyloid plaque
+ deposition occurs. In the absence of calcium, protofibrils can
+ remain stable in vitro for several days. Using this approach, we
+ directly compared the neurotoxicity of protofibrils and mature
+ amyloid fibrils and demonstrate that both species are inherently
+ toxic to neurons in culture. Thus, calcium may be an important
+ predisposing factor for Abeta aggregation and toxicity. The high
+ extracellular concentration of calcium in the brain, together with
+ impaired intraneuronal calcium regulation in the aging brain and
+ Alzheimer disease, may play an important role in the onset of
+ amyloid-related pathology.},
+}
+
+@article{ itkin2011,
+ author = AItkin #" and "# VDupres #" and "# YFDufrene #" and "#
+ BBechinger #" and "# JMRuysschaert #" and "# VRaussens,
+ title = {Calcium ions promote formation of amyloid $\beta$-peptide
+ (1-40) oligomers causally implicated in neuronal toxicity of
+ {A}lzheimer's disease.},
+ year = 2011,
+ month = mar,
+ day = 28,
+ address = {Laboratory of Structure and Function of Biological
+ Membranes, Center for Structural Biology and
+ Bioinformatics, Universit{\'e} Libre de Bruxelles,
+ Brussels, Belgium.},
+ journal = PLOS:ONE,
+ volume = 6,
+ number = 3,
+ pages = {e18250},
+ keywords = {Alzheimer Disease},
+ keywords = {Amyloid beta-Peptides},
+ keywords = {Blotting, Western},
+ keywords = {Calcium},
+ keywords = {Fluorescence},
+ keywords = {Humans},
+ keywords = {Ions},
+ keywords = {Models, Biological},
+ keywords = {Mutant Proteins},
+ keywords = {Neurons},
+ keywords = {Protein Structure, Quaternary},
+ keywords = {Protein Structure, Secondary},
+ keywords = {Spectroscopy, Fourier Transform Infrared},
+ keywords = {Thiazoles},
+ ISSN = {1932-6203},
+ doi = {10.1371/journal.pone.0018250},
+ URL = {http://www.ncbi.nlm.nih.gov/pubmed/21464905},
+ language = {eng},
+ abstract = {Amyloid $\beta$-peptide (A$\beta$) is directly linked to
+ Alzheimer's disease (AD). In its monomeric form, A$\beta$
+ aggregates to produce fibrils and a range of oligomers, the latter
+ being the most neurotoxic. Dysregulation of Ca(2+) homeostasis in
+ aging brains and in neurodegenerative disorders plays a crucial
+ role in numerous processes and contributes to cell dysfunction and
+ death. Here we postulated that calcium may enable or accelerate
+ the aggregation of A$\beta$. We compared the aggregation pattern
+ of A$\beta$(1-40) and that of A$\beta$(1-40)E22G, an amyloid
+ peptide carrying the Arctic mutation that causes early onset of
+ the disease. We found that in the presence of Ca(2+),
+ A$\beta$(1-40) preferentially formed oligomers similar to those
+ formed by A$\beta$(1-40)E22G with or without added Ca(2+), whereas
+ in the absence of added Ca(2+) the A$\beta$(1-40) aggregated to
+ form fibrils. Morphological similarities of the oligomers were
+ confirmed by contact mode atomic force microscopy imaging. The
+ distribution of oligomeric and fibrillar species in different
+ samples was detected by gel electrophoresis and Western blot
+ analysis, the results of which were further supported by
+ thioflavin T fluorescence experiments. In the samples without
+ Ca(2+), Fourier transform infrared spectroscopy revealed
+ conversion of oligomers from an anti-parallel $\beta$-sheet to the
+ parallel $\beta$-sheet conformation characteristic of
+ fibrils. Overall, these results led us to conclude that calcium
+ ions stimulate the formation of oligomers of A$\beta$(1-40), that
+ have been implicated in the pathogenesis of AD.},
+}
+
+@article{ zidar11,
+ author = JZidar #" and "# FMerzel,
+ title = {Probing amyloid-beta fibril stability by increasing ionic
+ strengths.},
+ year = 2011,
+ month = mar,
+ day = 10,
+ address = {National Institute of Chemistry, Hajdrihova 19,
+ SI-1000 Ljubljana, Slovenia.},
+ journal = JPC:B,
+ volume = 115,
+ number = 9,
+ pages = {2075--2081},
+ issn = {1520-5207},
+ doi = {10.1021/jp109025b},
+ URL = {http://www.ncbi.nlm.nih.gov/pubmed/21329333},
+ language = {eng},
+ keywords = {Amyloid beta-Peptides},
+ keywords = {Entropy},
+ keywords = {Hydrogen Bonding},
+ keywords = {Molecular Dynamics Simulation},
+ keywords = {Osmolar Concentration},
+ keywords = {Protein Multimerization},
+ keywords = {Protein Stability},
+ keywords = {Protein Structure, Secondary},
+ keywords = {Solvents},
+ keywords = {Vibration},
+ abstract = {Previous experimental studies have demonstrated changing
+ the ionic strength of the solvent to have a great impact on the
+ mechanism of aggregation of amyloid-beta (A$\beta$) protein
+ leading to distinct fibril morphology at high and low ionic
+ strength. Here, we use molecular dynamics simulations to elucidate
+ the ionic strength-dependent effects on the structure and dynamics
+ of the model A$\beta$ fibril. The change in ionic strength was
+ brought forth by varying the NaCl concentration in the environment
+ surrounding the A$\beta$ fibril. Comparison of the calculated
+ vibrational spectra of A$\beta$ derived from 40 ns all-atom
+ molecular dynamics simulations at different ionic strength reveals
+ the fibril structure to be stiffer with increasing ionic
+ strength. This finding is further corroborated by the calculation
+ of the stretching force constants. Decomposition of binding and
+ dynamical properties into contributions from different structural
+ segments indicates the elongation of the fibril at low ionic
+ strength is most likely promoted by hydrogen bonding between
+ N-terminal parts of the fibril, whereas aggregation at higher
+ ionic strength is suggested to be driven by the hydrophobic
+ interaction.},
+}
+
+@article{ miao11,
+ author = LMiao #" and "# HQin #" and "# PKoehl #" and "# JSong,
+ title = {Selective and specific ion binding on proteins at
+ physiologically-relevant concentrations.},
+ year = 2011,
+ month = oct,
+ day = 03,
+ address = {Department of Biological Sciences, Faculty of Science,
+ National University of Singapore, Singapore.},
+ journal = FEBS,
+ volume = 585,
+ number = 19,
+ pages = {3126--3132},
+ issn = {1873-3468},
+ doi = {10.1016/j.febslet.2011.08.048},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/21907714},
+ language = {eng},
+ keywords = {Amino Acid Sequence},
+ keywords = {Ephrin-B2},
+ keywords = {Ions},
+ keywords = {Models, Molecular},
+ keywords = {Molecular Sequence Data},
+ keywords = {Nuclear Magnetic Resonance, Biomolecular},
+ keywords = {Protein Binding},
+ keywords = {Protein Folding},
+ keywords = {Protein Structure, Tertiary},
+ keywords = {Salts},
+ keywords = {Solutions},
+ keywords = {Thermodynamics},
+ keywords = {Water},
+ abstract = {Insoluble proteins dissolved in unsalted water appear to
+ have no well-folded tertiary structures. This raises a fundamental
+ question as to whether being unstructured is due to the absence of
+ salt ions. To address this issue, we solubilized the insoluble
+ ephrin-B2 cytoplasmic domain in unsalted water and first confirmed
+ using NMR spectroscopy that it is only partially folded. Using NMR
+ HSQC titrations with 14 different salts, we further demonstrate
+ that the addition of salt triggers no significant folding of the
+ protein within physiologically relevant ion concentrations. We
+ reveal however that their 8 anions bind to the ephrin-B2 protein
+ with high affinity and specificity at biologically-relevant
+ concentrations. Interestingly, the binding is found to be both
+ salt- and residue-specific.},
+}
projects / thesis.git / commitdiff