From: W. Trevor King Date: Mon, 20 May 2013 16:37:55 +0000 (-0400) Subject: root.bib: Add chauhan97, friedman05, friedman11, zhang06, ... X-Git-Tag: v1.0~155 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=6c9b74ff5b79120e2deead69db1eaa41c6859643;p=thesis.git root.bib: Add chauhan97, friedman05, friedman11, zhang06, ... Also isaacs06, itkin2011, zidar11, and miao11. Micholas Smith suggested these for background information on the effect of ions on protein binding. They focus on Aβ aggregation, but the general ideas should be the same. --- diff --git a/src/root.bib b/src/root.bib index ddc40dc..76416b1 100644 --- a/src/root.bib +++ b/src/root.bib @@ -78,6 +78,7 @@ @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."} @@ -171,6 +172,8 @@ @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"} @@ -219,10 +222,12 @@ @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."} @@ -265,9 +270,11 @@ @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."} @@ -311,6 +318,7 @@ @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"} @@ -371,6 +379,7 @@ @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"} @@ -460,8 +469,10 @@ @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."} @@ -542,6 +553,7 @@ @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"} @@ -679,10 +691,12 @@ @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."} @@ -717,6 +731,7 @@ @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"} @@ -735,6 +750,7 @@ @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"} @@ -803,6 +819,8 @@ @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."} @@ -820,6 +838,7 @@ @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."} @@ -830,6 +849,8 @@ @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."} @@ -864,6 +885,7 @@ @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."} @@ -905,6 +927,7 @@ @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"} @@ -918,6 +941,7 @@ @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."} @@ -943,6 +967,7 @@ @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."} @@ -989,6 +1014,7 @@ @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"} @@ -1060,6 +1086,7 @@ @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."} @@ -1089,6 +1116,7 @@ @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."} @@ -1113,6 +1141,7 @@ @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."} @@ -1122,6 +1151,7 @@ @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."} @@ -1130,6 +1160,7 @@ @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"} @@ -1145,6 +1176,7 @@ @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."} @@ -10369,3 +10401,411 @@ 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.}, +}