From 97c7a873c73ea19a93c479a162de85a3c6a9f126 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Sat, 23 Oct 2010 13:57:16 -0400 Subject: [PATCH] Start fleshing out "Related work" section in the manual. To facilitate this, I've added the following new keys to sawsim.bib: jollymore09, kellermayer97, king10, marszalek98, oberhauser98, rief97a I also renamed the old rief97 -> rief97b to avoid confusion with rief97a. Also, run a second bibtex/pdflatex pass on compilation to handle a single layer of cross referencing in the `note` field. --- src/sawsim.bib | 281 +++++++++++++++++++++++++++++++++++++++++++++---- src/sawsim.nw | 28 ++++- 2 files changed, 289 insertions(+), 20 deletions(-) diff --git a/src/sawsim.bib b/src/sawsim.bib index 948c196..417de25 100644 --- a/src/sawsim.bib +++ b/src/sawsim.bib @@ -101,7 +101,7 @@ @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}} @@ -127,6 +127,7 @@ @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"} @@ -138,13 +139,16 @@ @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."} @@ -168,6 +172,7 @@ @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"} @@ -202,6 +207,7 @@ @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"} @@ -227,6 +233,7 @@ @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"} @@ -270,7 +277,7 @@ @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"} @@ -280,7 +287,7 @@ @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."} @@ -288,6 +295,7 @@ @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"} @@ -447,7 +455,7 @@ year = 1978, month = may, day = 12, - journal = Science, + journal = SCI, volume = 200, number = 4342, pages = "618--627", @@ -480,6 +488,8 @@ 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, @@ -702,12 +712,12 @@ @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", @@ -1584,6 +1594,54 @@ 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 @@ -1620,6 +1678,41 @@ 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} @@ -1630,6 +1723,43 @@ 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 @@ -1776,7 +1906,7 @@ @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, @@ -1952,6 +2082,43 @@ 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, @@ -2287,6 +2454,50 @@ 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, @@ -2627,23 +2838,54 @@ 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" } @@ -2661,7 +2903,10 @@ 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, diff --git a/src/sawsim.nw b/src/sawsim.nw index f70f986..c4ba071 100644 --- a/src/sawsim.nw +++ b/src/sawsim.nw @@ -127,7 +127,29 @@ to share the burden and increase the transparency of data analysis. \subsection{Related work} -TODO References +Sawim has been published\citep{king10}! It is, as far as I know, the +only open-source Monte Carlo force spectroscopy simulator, but similar +closed source simulators have been around since the seminal paper by +\citet{rief97a}. In chronological order, major contributions have +come from + +\begin{packed_item} + \item \citet{rief97a} \citeyear{rief97a}: + \item \citet{rief97b} \citeyear{rief97b}: + \item \citet{kellermayer97} \citeyear{kellermayer97}: + \item \citet{rief98} \citeyear{rief98}: + first paper to focus mainly on the simulation + \item \citet{oberhauser98} \citeyear{oberhauser98}: + \item \citet{carrion-vazquez99a} \citeyear{carrion-vazquez99a}: + \item \citet{best02} \citeyear{best02}: + pointed out large fit valley + \item \citet{zinober02} \citeyear{zinober02}: + introduced the scaffold effect + \item \citet{jollymore09} \citeyear{jollymore09}: + \item \citet{king10} \citeyear{king10}: + introduced sawsim +\end{packed_item} + \subsection{About this document} @@ -6531,6 +6553,8 @@ $(DOC_DIR)/sawsim.pdf : $(BUILD_DIR)/sawsim.tex $(BUILD_DIR)/sawsim.bib \ $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim" $(SHELL) -e -c "cd $(BUILD_DIR) && bibtex sawsim" $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim" + $(SHELL) -e -c "cd $(BUILD_DIR) && bibtex sawsim" + $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim" $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim" mv $(BUILD_DIR)/sawsim.pdf $@ @ @@ -6626,7 +6650,7 @@ clean : $(CHECK_BINS:%=clean_%) $(SAWSIM_MODS:%=clean_%) \ $(BUILD_DIR)/interp.c $(BUILD_DIR)/interp.h \ $(BUILD_DIR)/tavl.c $(BUILD_DIR)/tavl.h \ $(BUILD_DIR)/global.h ./gmon.out - $(SHELL) -e -c "rmdir $(BUILD_DIR) $(BIN_DIR) $(DOC_DIR)" + $(SHELL) -e -c "rmdir $(BUILD_DIR) $(DOC_DIR)" # Various builds of sawsim $(BIN_DIR)/sawsim : $(SAWSIM_SRC) | $(BIN_DIR) -- 2.26.2