@string{JGlaser = "Glaser, Jens"}
@string{BGompertz = "Gompertz, Benjamin"}
@string{BGough = "Gough, Brian"}
-@string{HGranzier = "Granzier, Henk"}
+@string{HLGranzier = "Granzier, Henk L."}
@string{FGrater = "Grater, Frauke"}
@string{CGrossman = "Grossman, C."}
@string{HGrubmuller = {Grubm{\"u}ller, Helmut}}
@string{WLHung = "Hung, Wen-Liang"}
@string{JLHutter = "Hutter, Jeffrey L."}
@string{CHyeon = "Hyeon, Changbong"}
+@string{IJBMM = "International Journal of Biological Macromolecules"}
@string{AIrback = "Irback, Anders"}
@string{SIzrailev = "Izrailev, S."}
@string{JBiotechnol = "J Biotechnol"}
@string{YJia = "Jia, Yiwei"}
@string{SJiang = "Jiang, Shaoyi"}
@string{CPJohnson = "Johnson, Colin P."}
+@string{AJollymore = "Jollymore, Ashlee"}
@string{EJones = "Jones, Eric"}
+@string{JMB = "Journal of Molecular Biology"}
@string{DAJuckett = "Juckett, D. A."}
@string{GJungman = "Jungman, Gerard"}
@string{DKaftan = "Kaftan, David"}
@string{RKapon = "Kapon, Ruti"}
@string{AKardinal = "Kardinal, Angelika"}
@string{MKarplus = "Karplus, Martin"}
+@string{MSZKellermayer = "Kellermayer, Mikl\'os S. Z."}
@string{FKienberger = "Kienberger, Ferry"}
@string{WTKing = "King, W. Trevor"}
@string{JKlafter = "Klafter, J."}
@string{SLee = "Lee, Sunyoung"}
@string{RLemmen = "Lemmen, Robert"}
@string{OLequin = "Lequin, Olivier"}
+@string{CLethias = "Lethias, Claire"}
@string{HLi = "Li, Hongbin"}
@string{MSLi = "Li, Mai Suan"}
@string{FCLin = "Lin, Fan-Chi"}
@string{VMontana = "Montana, Vedrana"}
@string{LMontanaro = "Montanaro, Lucio"}
@string{SMukamel = "Mukamel, Shaul"}
+@string{NAT = "Nature"}
@string{NSB = "Nat Struct Biol"}
@string{NSMB = "Nat Struct Mol Biol"}
@string{CNeagoe = "Neagoe, Ciprian"}
@string{EOroudjev = "Oroudjev, E."}
@string{OUP = "Oxford University Press"}
@string{EPaci = "Paci, Emanuele"}
+@string{YPPang = "Pang, Y. P."}
@string{VParpura = "Parpura, Vladimir"}
@string{QPeng = "Peng, Qing"}
@string{OPerisic = "Perisic, Ognjen"}
@string{KSchulten = "Schulten, Klaus"}
@string{ZSchulten = "Schulten, Zan"}
@string{ISchwaiger = "Schwaiger, Ingo"}
-@string{Science = "Science"}
+@string{SCI = "Science"}
@string{USeifert = "Seifert, Udo"}
@string{BSenger = "Senger, B."}
@string{EShakhnovich = "Shakhnovich, Eugene"}
@string{EDSiggia = "Siggia, Eric D."}
@string{CLSmith = "Smith, Corey L."}
@string{DASmith = "Smith, D. Alastair"}
-@string{SSmith = "Smith, S."}
+@string{SBSmith = "Smith, S. B."}
@string{JSoares = "Soares, J."}
@string{NDSocci = "Socci, N. D."}
@string{DWSpeicher = "Speicher, David W."}
@string{AStout = "Stout, A."}
@string{CStroh = "Stroh, Cordula"}
@string{TStrunz = "Strunz, Torsten"}
+@string{MSu = "Su, Meihong"}
@string{ASzabo = "Szabo, Attila"}
@string{DSTalaga = "Talaga, David S."}
@string{PTalkner = "Talkner, Peter"}
year = 1978,
month = may,
day = 12,
- journal = Science,
+ journal = SCI,
volume = 200,
number = 4342,
pages = "618--627",
title = "{A simple method for probing the mechanical unfolding pathway of
proteins in detail}",
year = 2002,
+ month = sep,
+ day = 17,
journal = PNAS,
volume = 99,
number = 19,
@article { bustamante94,
author = CBustamante #" and "# JFMarko #" and "# EDSiggia #" and "#
- SSmith,
+ SBSmith,
title = "Entropic elasticity of lambda-phage {DNA}.",
year = 1994,
month = sep,
day = 09,
- journal = Science,
+ journal = SCI,
volume = 265,
number = 5178,
pages = "1599--1600",
rupture."
}
+@article { jollymore09,
+ author = AJollymore #" and "# CLethias #" and "# QPeng #" and "# YCao #"
+ and "# HLi,
+ title = "Nanomechanical properties of tenascin-{X} revealed by single-
+ molecule force spectroscopy",
+ year = 2009,
+ month = jan,
+ day = 30,
+ journal = JMB,
+ volume = 385,
+ number = 4,
+ pages = "1277--1286",
+ issn = "1089-8638",
+ doi = "10.1016/j.jmb.2008.11.038",
+ url = "http://dx.doi.org/10.1016/j.jmb.2008.11.038",
+ keywords = "Animals;Biomechanics;Cattle;Fibronectins;Kinetics;Microscopy,
+ Atomic Force;Protein Folding;Protein Structure, Tertiary;Spectrum
+ Analysis;Tenascin",
+ abstract = "Tenascin-X is an extracellular matrix protein and binds a
+ variety of molecules in extracellular matrix and on cell membrane.
+ Tenascin-X plays important roles in regulating the structure and
+ mechanical properties of connective tissues. Using single-molecule
+ atomic force microscopy, we have investigated the mechanical properties
+ of bovine tenascin-X in detail. Our results indicated that tenascin-X
+ is an elastic protein and the fibronectin type III (FnIII) domains can
+ unfold under a stretching force and refold to regain their mechanical
+ stability upon the removal of the stretching force. All the 30 FnIII
+ domains of tenascin-X show similar mechanical stability, mechanical
+ unfolding kinetics, and contour length increment upon domain unfolding,
+ despite their large sequence diversity. In contrast to the homogeneity
+ in their mechanical unfolding behaviors, FnIII domains fold at
+ different rates. Using the 10th FnIII domain of tenascin-X (TNXfn10) as
+ a model system, we constructed a polyprotein chimera composed of
+ alternating TNXfn10 and GB1 domains and used atomic force microscopy to
+ confirm that the mechanical properties of TNXfn10 are consistent with
+ those of the FnIII domains of tenascin-X. These results lay the
+ foundation to further study the mechanical properties of individual
+ FnIII domains and establish the relationship between point mutations
+ and mechanical phenotypic effect on tenascin-X. Moreover, our results
+ provided the opportunity to compare the mechanical properties and
+ design of different forms of tenascins. The comparison between
+ tenascin-X and tenascin-C revealed interesting common as well as
+ distinguishing features for mechanical unfolding and folding of
+ tenascin-C and tenascin-X and will open up new avenues to investigate
+ the mechanical functions and architectural design of different forms of
+ tenascins."
+}
+
@article { juckett93,
author = DAJuckett #" and "# BRosenberg,
title = "Comparison of the Gompertz and Weibull functions as descriptors
Weibull models."
}
+@article { kellermayer97,
+ author = MSZKellermayer #" and "# SBSmith #" and "# HLGranzier #" and "#
+ CBustamante,
+ title = "Folding-unfolding transitions in single titin molecules
+ characterized with laser tweezers",
+ year = 1997,
+ month = may,
+ day = 16,
+ journal = SCI,
+ volume = 276,
+ number = 5315,
+ pages = "1112--1116",
+ issn = "0036-8075",
+ keywords = "Amino Acid
+ Sequence;Elasticity;Entropy;Immunoglobulins;Lasers;Models,
+ Chemical;Muscle Contraction;Muscle Proteins;Muscle Relaxation;Muscle,
+ Skeletal;Protein Denaturation;Protein Folding;Protein Kinases;Stress,
+ Mechanical",
+ abstract = "Titin, a giant filamentous polypeptide, is believed to play a
+ fundamental role in maintaining sarcomeric structural integrity and
+ developing what is known as passive force in muscle. Measurements of
+ the force required to stretch a single molecule revealed that titin
+ behaves as a highly nonlinear entropic spring. The molecule unfolds in
+ a high-force transition beginning at 20 to 30 piconewtons and refolds
+ in a low-force transition at approximately 2.5 piconewtons. A fraction
+ of the molecule (5 to 40 percent) remains permanently unfolded,
+ behaving as a wormlike chain with a persistence length (a measure of
+ the chain's bending rigidity) of 20 angstroms. Force hysteresis arises
+ from a difference between the unfolding and refolding kinetics of the
+ molecule relative to the stretch and release rates in the experiments,
+ respectively. Scaling the molecular data up to sarcomeric dimensions
+ reproduced many features of the passive force versus extension curve of
+ muscle fibers."
+}
+
@article { king09,
author = WTKing #" and "# GYang,
title = "Effects of Cantilever Stiffness on Unfolding Force in {AFM}
journal = BPS:P
}
+@article { king10,
+ author = WTKing #" and "# MSu #" and "# GYang,
+ title = "{M}onte {C}arlo simulation of mechanical unfolding of proteins
+ based on a simple two-state model",
+ year = 2010,
+ journal = IJBMM,
+ volume = 46,
+ number = 2,
+ pages = "159--166",
+ issn = "0141-8130",
+ doi = "10.1016/j.ijbiomac.2009.12.001",
+ url = "http://www.sciencedirect.com/science/article/B6T7J-4XWMND2-1/2/7ef768562b4157fc201d450553e5de5e",
+ keywords = "Atomic force microscopy;Mechanical unfolding;Monte Carlo
+ simulation;Worm-like chain;Single molecule methods",
+ abstract = "Single molecule methods are becoming routine biophysical
+ techniques for studying biological macromolecules. In mechanical
+ unfolding of proteins, an externally applied force is used to induce
+ the unfolding of individual protein molecules. Such experiments have
+ revealed novel information that has significantly enhanced our
+ understanding of the function and folding mechanisms of several types
+ of proteins. To obtain information on the unfolding kinetics and the
+ free energy landscape of the protein molecule from mechanical unfolding
+ data, a Monte Carlo simulation based on a simple two-state kinetic
+ model is often used. In this paper, we provide a detailed description
+ of the procedure to perform such simulations and discuss the
+ approximations and assumptions involved. We show that the appearance of
+ the force versus extension curves from mechanical unfolding of proteins
+ is affected by a variety of experimental parameters, such as the length
+ of the protein polymer and the force constant of the cantilever. We
+ also analyze the errors associated with different methods of data
+ pooling and present a quantitative measure of how well the simulation
+ results fit experimental data. These findings will be helpful in
+ experimental design, artifact identification, and data analysis for
+ single molecule studies of various proteins using the mechanical
+ unfolding method."
+}
+
@article { kleiner07,
author = AKleiner #" and "# EShakhnovich,
title = "The mechanical unfolding of ubiquitin through all-atom Monte Carlo
@article { labeit03,
author = DLabeit #" and "# KWatanabe #" and "# CWitt #" and "# HFujita #"
and "# YWu #" and "# SLahmers #" and "# TFunck #" and "# SLabeit #" and
- "# HGranzier,
+ "# HLGranzier,
title = "Calcium-dependent molecular spring elements in the giant protein
titin",
year = 2003,
note = "Derivation of the Worm-like Chain interpolation function."
}
+@article { marszalek98,
+ author = PEMarszalek #" and "# AFOberhauser #" and "# YPPang #" and "#
+ JMFernandez,
+ title = "Polysaccharide elasticity governed by chair-boat transitions of
+ the glucopyranose ring.",
+ year = 1998,
+ month = dec,
+ day = 17,
+ journal = NAT,
+ volume = 396,
+ number = 6712,
+ pages = "661--664",
+ issn = "0028-0836",
+ doi = "10.1038/25322",
+ keywords = "Amylose;Dextrans;Elasticity;Glucans;Glucose;Microscopy, Atomic
+ Force;Oxidation-Reduction;Polysaccharides",
+ abstract = "Many common, biologically important polysaccharides contain
+ pyranose rings made of five carbon atoms and one oxygen atom. They
+ occur in a variety of cellular structures, where they are often
+ subjected to considerable tensile stress. The polysaccharides are
+ thought to respond to this stress by elastic deformation, but the
+ underlying molecular rearrangements allowing such a response remain
+ poorly understood. It is typically assumed, however, that the pyranose
+ ring structure is inelastic and locked into a chair-like conformation.
+ Here we describe single-molecule force measurements on individual
+ polysaccharides that identify the pyranose rings as the structural unit
+ controlling the molecule's elasticity. In particular, we find that the
+ enthalpic component of the polymer elasticity of amylose, dextran and
+ pullulan is eliminated once their pyranose rings are cleaved. We
+ interpret these observations as indicating that the elasticity of the
+ three polysaccharides results from a force-induced elongation of the
+ ring structure and a final transition from a chair-like to a boat-like
+ conformation. We expect that the force-induced deformation of pyranose
+ rings reported here plays an important role in accommodating mechanical
+ stresses and modulating ligand binding in biological systems."
+}
+
@article { marszalek02,
author = PEMarszalek #" and "# HLi #" and "# AFOberhauser #" and "#
JMFernandez,
under different conditions."
}
+@article { oberhauser98,
+ author = AFOberhauser #" and "# PEMarszalek #" and "# HPErickson #" and "#
+ JMFernandez,
+ title = "The molecular elasticity of the extracellular matrix protein
+ tenascin.",
+ year = 1998,
+ month = may,
+ day = 14,
+ journal = NAT,
+ volume = 393,
+ number = 6681,
+ pages = "181--185",
+ issn = "0028-0836",
+ doi = "10.1038/30270",
+ eprint = "http://www.nature.com/nature/journal/v393/n6681/pdf/393181a0.pdf",
+ url = "http://www.nature.com/nature/journal/v393/n6681/abs/393181a0.html",
+ keywords = "Alternative Splicing;Binding
+ Sites;Elasticity;Fibronectins;Humans;Microscopy, Atomic Force;Monte
+ Carlo Method;Peptide Fragments;Protein Folding;Recombinant
+ Proteins;Tenascin",
+ abstract = "Extracellular matrix proteins are thought to provide a rigid
+ mechanical anchor that supports and guides migrating and rolling cells.
+ Here we examine the mechanical properties of the extracellular matrix
+ protein tenascin by using atomic-force-microscopy techniques. Our
+ results indicate that tenascin is an elastic protein. Single molecules
+ of tenascin could be stretched to several times their resting length.
+ Force-extension curves showed a saw-tooth pattern, with peaks of force
+ at 137pN. These peaks were approximately 25 nm apart. Similar results
+ have been obtained by study of titin. We also found similar results by
+ studying recombinant tenascin fragments encompassing the 15 fibronectin
+ type III domains of tenascin. This indicates that the extensibility of
+ tenascin may be due to the stretch-induced unfolding of its fibronectin
+ type III domains. Refolding of tenascin after stretching, observed when
+ the force was reduced to near zero, showed a double-exponential
+ recovery with time constants of 42 domains refolded per second and 0.5
+ domains per second. The former speed of refolding is more than twice as
+ fast as any previously reported speed of refolding of a fibronectin
+ type III domain. We suggest that the extensibility of the modular
+ fibronectin type III region may be important in allowing
+ tenascin-ligand bonds to persist over long extensions. These properties
+ of fibronectin type III modules may be of widespread use in
+ extracellular proteins containing such domain."
+}
+
@article { oberhauser01,
author = AFOberhauser #" and "# PKHansma #" and "# MCarrion-Vazquez #" and
"# JMFernandez,
project = "Cantilever Calibration"
}
-@article { rief97,
- author = MRief #" and "# MGautel #" and "# FOesterhelt #" and "#
- JMFernandez #" and "# HEGaub,
- title = "{Reversible Unfolding of Individual Titin Immunoglobulin Domains
- by AFM}",
+@article { rief97a,
+ author = MRief #" and "# FOesterhelt #" and "# BHeymann #" and "# HEGaub,
+ title = "Single Molecule Force Spectroscopy on Polysaccharides by Atomic
+ Force Microscopy",
year = 1997,
- journal = Science,
+ month = feb,
+ day = 28,
+ journal = SCI,
+ volume = 275,
+ number = 5304,
+ pages = "1295--1297",
+ issn = "1095-9203",
+ doi = "10.1126/science.275.5304.1295",
+ eprint = "http://www.sciencemag.org/cgi/reprint/275/5304/1295.pdf",
+ url = "http://www.sciencemag.org/cgi/content/abstract/275/5304/1295",
+ abstract = "Recent developments in piconewton instrumentation allow the
+ manipulation of single molecules and measurements of intermolecular as
+ well as intramolecular forces. Dextran filaments linked to a gold
+ surface were probed with the atomic force microscope tip by vertical
+ stretching. At low forces the deformation of dextran was found to be
+ dominated by entropic forces and can be described by the Langevin
+ function with a 6 angstrom Kuhn length. At elevated forces the strand
+ elongation was governed by a twist of bond angles. At higher forces the
+ dextran filaments underwent a distinct conformational change. The
+ polymer stiffened and the segment elasticity was dominated by the
+ bending of bond angles. The conformational change was found to be
+ reversible and was corroborated by molecular dynamics calculations."
+}
+
+@article { rief97b,
+ author = MRief #" and "# MGautel #" and "# FOesterhelt #" and "# JMFernandez
+ #" and "# HEGaub,
+ title = "Reversible Unfolding of Individual Titin Immunoglobulin Domains by
+ {AFM}",
+ year = 1997,
+ month = may,
+ day = 16,
+ journal = SCI,
volume = 276,
number = 5315,
pages = "1109--1112",
doi = "10.1126/science.276.5315.1109",
eprint = "http://www.sciencemag.org/cgi/reprint/276/5315/1109.pdf",
url = "http://www.sciencemag.org/cgi/content/abstract/276/5315/1109",
- note = "Seminal paper for force spectroscopy on Titin. Cited by Dietz
- '04\cite{dietz04} (ref 9) as an example of how unfolding large proteins
- is easily interpreted (vs. confusing unfolding in bulk), but Titin is a
- rather simple example of that, because of it's globular-chain
+ note = "Seminal paper for force spectroscopy on Titin. Cited by
+ \citet{dietz04} (ref 9) as an example of how unfolding large proteins
+ is easily interpreted (vs.\ confusing unfolding in bulk), but Titin is
+ a rather simple example of that, because of its globular-chain
structure.",
project = "Energy Landscape Roughness"
}
numpages = 3,
publisher = APS,
doi = "10.1103/PhysRevLett.81.4764",
- eprint = "http://prola.aps.org/pdf/PRL/v81/i21/p4764_1"
+ eprint = "http://prola.aps.org/pdf/PRL/v81/i21/p4764_1",
+ url = "http://prola.aps.org/abstract/PRL/v81/i21/p4764_1",
+ note = "Original details on mechanical unfolding analysis via Monte Carlo
+ simulation."
}
@article { sarkar04,
projects / sawsim.git / commitdiff