Research Topics
| CARLOS JOSE BUSTAMANTESummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
Grabbing the cat by the tail: manipulating molecules one by oneC Bustamante
Howard Hughes Medical Institute, Berkeley, California, USA
Nat Rev Mol Cell Biol 1:130-6. 2000..We describe here the physical principles behind these methods, and discuss their capabilities and current limitations...
In singulo biochemistry: when less is moreCarlos Bustamante
Department of Physics and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
Annu Rev Biochem 77:45-50. 2008..We discuss here some of the advantages of single-molecule methods over their bulk counterparts and argue that these advantages should help establish them as essential tools in the technical arsenal of the modern biochemist...
Of torques, forces, and protein machinesCarlos Bustamante
Department of Physics, University of California at Berkeley, Berkeley, CA 94720-7300, USA
Protein Sci 13:3061-5. 2004- Revisiting the central dogma one molecule at a timeCarlos Bustamante
Jason L Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, 94720, USA
Cell 144:480-97. 2011..Here we present an overview of the main results arrived at by the application of single-molecule methods to the study of the main machines of the central dogma... - Mechanical processes in biochemistryCarlos Bustamante
Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, California 94720 3206, USA
Annu Rev Biochem 73:705-48. 2004..This review provides the conceptual framework to understand the role of mechanical force in biochemistry... - Ten years of tension: single-molecule DNA mechanicsCarlos Bustamante
Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
Nature 421:423-7. 2003..These studies have illuminated the nature of interactions between DNA and proteins, the constraints within which the cellular machinery operates, and the forces created by DNA-dependent motors... - Unfolding single RNA molecules: bridging the gap between equilibrium and non-equilibrium statistical thermodynamicsCarlos Bustamante
Department of Physics, Lawrence Berkeley National Laboratory Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
Q Rev Biophys 38:291-301. 2005..It is perhaps a sign of the times that important physical results are these days used to extract information about biological systems and that biological systems are being used to test and confirm fundamental new laws in physics... - Determination of thermodynamics and kinetics of RNA reactions by forceIgnacio Tinoco
Department of Chemistry, University of California, Berkeley, CA 94720 1460, USA
Q Rev Biophys 39:325-60. 2006..Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force... - Proofreading dynamics of a processive DNA polymeraseBorja Ibarra
Department of Physics, University of California, Berkeley, CA 94720 3220, USA
EMBO J 28:2794-802. 2009..The primer transfer is achieved through two novel intermediates, one a tension-sensitive and functional polymerization conformation and a second non-active state that may work as a fidelity check point for the proofreading reaction... - Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured resultsJin Der Wen
Department of Chemistry, University of California, Berkeley, California, USA
Biophys J 92:2996-3009. 2007..In the companion article on pages 3010-3021, we analyze how the measured kinetics parameters differ from the intrinsic molecular rates of the RNA, and thus how to obtain the molecular rates... - DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSCYongli Zhang
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
Mol Cell 24:559-68. 2006..Such loop formation may provide a molecular basis for the biological functions of remodelers... - RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATPSophie Dumont
Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
Nature 439:105-8. 2006..The assay developed here should be useful in investigating a broad range of nucleic acid translocation motors... - Molecular handles for the mechanical manipulation of single-membrane proteins in living cellsPau Gorostiza
Departments of Physics and Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
IEEE Trans Nanobioscience 4:269-76. 2005..Binding forces of approximately 80 pN at 100 nN/s were measured... - Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction methodAndres E Leschziner
Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 104:4913-8. 2007..We present a model of the RSC-nucleosome complex that rationalizes the single molecule results obtained by using optical tweezers and also discuss the mechanistic implications of our structures... - Measurement of the effect of monovalent cations on RNA hairpin stabilityJeffrey Vieregg
Department of Physics, University of California, Berkeley, California 94720, USA
J Am Chem Soc 129:14966-73. 2007..Surprisingly, the U.C.U bulge of TAR was found to be equally stable in all conditions tested. We also report a new estimate for the elastic parameters of single-stranded RNA... - Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methodsPan T X Li
Department of Chemistry, University of California, Berkeley, California, USA
Biophys J 90:250-60. 2006..Thus, we find that folding of RNA hairpins can be more complex than a simple single-step reaction, and that application of several methods can improve understanding of reaction mechanisms... - Characterization of the mechanical unfolding of RNA pseudoknotsLisa Green
Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
J Mol Biol 375:511-28. 2008..The greater mechanical stability of pseudoknots compared to hairpins, and their kinetic insensitivity to force supports the hypothesis that -1 frameshifting depends on the difficulty of unfolding the mRNA... - Coupling translocation with nucleic acid unwinding by NS3 helicaseJin Yu
Department of Physics, University of California, Berkeley, CA 94720, USA
J Mol Biol 404:439-55. 2010..The generic features of coupling single-stranded nucleic acid translocation with duplex unwinding presented in this work may apply generally to a class of helicases... - Recent advances in optical tweezersJeffrey R Moffitt
Department of Physics, University of California, Berkeley, CA 94720, USA
Annu Rev Biochem 77:205-28. 2008..In this review, we address these recent advances and speculate on possible future developments... - Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equalityJan Liphardt
Department of Chemistry, Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
Science 296:1832-5. 2002..This work also extends the thermodynamic analysis of single molecule manipulation data beyond the context of equilibrium experiments... - Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp bindingEric R Goedken
Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
J Mol Biol 336:1047-59. 2004.... - Real-time control of the energy landscape by force directs the folding of RNA moleculesPan T X Li
Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 104:7039-44. 2007..Controlling folding pathways at the single-molecule level provides a way to survey the manifold of folding trajectories and intermediates, a capability that previously was available only to theoretical studies... - NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening forkWei Cheng
QB3 Institute, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 104:13954-9. 2007..Instead, we find that NS3 destabilizes the duplex before separating the strands. Failure to do so before a strong barrier leads to helicase dissociation and limits the processivity of the enzyme... - Substrate interactions and promiscuity in a viral DNA packaging motorK Aathavan
Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
Nature 461:669-73. 2009..Such promiscuous, nonspecific contacts may reflect common translocase-substrate interactions for both the nucleic acid and protein translocases of the ASCE superfamily... - Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase IICourtney Hodges
Jason L Choy Laboratory of Single Molecule Biophysics and Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
Science 325:626-8. 2009..The interplay between polymerase dynamics and nucleosome fluctuations provides a physical basis for the regulation of eukaryotic transcription... - Protein-DNA chimeras for single molecule mechanical folding studies with the optical tweezersCiro Cecconi
Department of Molecular and Cell Biology, Institute for Quantitative Biology, University of California Berkeley, Berkeley, CA 94720 3220, USA
Eur Biophys J 37:729-38. 2008..It represents a new strategy to study protein folding at the single molecule level, and should be applicable to a range of problems requiring tethering of protein molecules... - Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuationsJeffrey R Moffitt
Department of Physics, University of California, Berkeley, 94720, USA
Proc Natl Acad Sci U S A 107:15739-44. 2010.... - Guanosine triphosphate acts as a cofactor to promote assembly of initial P-element transposase-DNA synaptic complexesMei Tang
Division of Genetics, Genomics and Development, Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
Genes Dev 19:1422-5. 2005..This initial complex then randomly and independently cleaves each P-element end. These data show that GTP acts to promote protein-DNA assembly, and may explain why P-element excision often leads to unidirectional deletions... - Unusual mechanical stability of a minimal RNA kissing complexPan T X Li
Department of Chemistry, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 103:15847-52. 2006..The strong mechanical stability of even a minimal kissing complex indicates the importance of such loop-loop interactions in initiating and stabilizing RNA dimers in retroviruses... - Effect of force on mononucleosomal dynamicsShirley Mihardja
Department of Chemistry, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 103:15871-6. 2006..These findings are needed to understand the energetics of nucleosome remodeling... - Sequence-directed DNA translocation by purified FtsKPaul J Pease
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3204, USA
Science 307:586-90. 2005..coli chromosome, as it does in vivo. Our results imply that FtsK is a bidirectional motor that changes direction in response to short, asymmetric directing DNA sequences... - The bacterial condensin MukBEF compacts DNA into a repetitive, stable structureRyan B Case
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
Science 305:222-7. 2004..We suggest a new model for how MukBEF organizes the bacterial chromosome in vivo... - Structural transitions and elasticity from torque measurements on DNAZev Bryant
Department of Molecular and Cell Biology, Department of Physics, Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
Nature 424:338-41. 2003..We also show that cooperative structural transitions in DNA can be exploited to construct constant-torque wind-up motors and force-torque converters... - Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerasesMichael D Stone
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 100:8654-9. 2003..Single-enzyme braid relaxation experiments also provide a direct measure of the processivity of the enzyme and offer insight into its mechanochemical cycle... - Mechanochemical analysis of DNA gyrase using rotor bead trackingJeff Gore
Department of Physics, University of California, Berkeley, California 94720, USA
Nature 439:100-4. 2006.... - DNA overwinds when stretchedJeff Gore
Department of Physics, University of California, Berkeley, California 94720, USA
Nature 442:836-9. 2006..The requisite coupled DNA distortions are favoured by the intrinsic mechanical properties of the double helix reported here... - Mechanochemistry of a viral DNA packaging motorJin Yu
Department of Physics, University of California, Berkeley, CA 94720, USA
J Mol Biol 400:186-203. 2010..The push and roll model provides a new perspective on how a multimeric ATPase transports DNA, and it might apply to other ring motors as well... - Methods in statistical kineticsJeffrey R Moffitt
Department of Physics and Jason L Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, California, USA
Methods Enzymol 475:221-57. 2010..The new kinetic parameters of this expression, akin to the Michaelis-Menten parameters, provide model-independent constraints on the kinetic mechanism... - The effect of force on thermodynamics and kinetics of single molecule reactionsIgnacio Tinoco
Department of Chemistry, University of California, Berkeley, CA 94720 1460, USA
Biophys Chem 101:513-33. 2002..Force changes the thermodynamic stability of a molecule; it can thus increase or decrease the free energy change for the reaction. Force can also speed or slow rates of reactions; it changes the free energy of activation of the reaction... - Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshiftingGang Chen
Department of Chemistry, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 106:12706-11. 2009..Better understanding of the molecular determinants of frameshifting efficiency may facilitate the development of anti-virus therapeutics targeting frameshifting... - Intersubunit coordination in a homomeric ring ATPaseJeffrey R Moffitt
Department of Physics and Jason L Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, California 94720, USA
Nature 457:446-50. 2009..Furthermore, a step size that is a non-integer number of base pairs demands new models for motor-DNA interactions... - Thermal probing of E. coli RNA polymerase off-pathway mechanismsYara X Mejia
Graduate Group in Applied Science and Technology, University of California, Berkeley, CA 94720, USA
J Mol Biol 382:628-37. 2008..This observation suggests that arrest could play a regulatory role in vivo, possibly through interactions with specific elongation factors... - Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymeraseNancy R Forde
The Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 99:11682-7. 2002.... - Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilisJerod L Ptacin
Department of Molecular and Cell Biology, 642 Stanley Hall, University of California, Berkeley, California 94720, USA
Nat Struct Mol Biol 15:485-93. 2008.... - Following translation by single ribosomes one codon at a timeJin Der Wen
Department of Chemistry, University of California, Berkeley, California 94720, USA
Nature 452:598-603. 2008..Translocation and RNA unwinding are strictly coupled ribosomal functions... - Backtracking determines the force sensitivity of RNAP II in a factor-dependent mannerEric A Galburt
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
Nature 446:820-3. 2007..4 pN. Taken together, these results describe a regulatory mechanism of transcription elongation in eukaryotes by which transcription factors modify the mechanical performance of RNAP II, allowing it to operate against higher loads... - Differential detection of dual traps improves the spatial resolution of optical tweezersJeffrey R Moffitt
Department of Physics, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 103:9006-11. 2006..Remarkably, we show that the spatial resolution of dual optical traps with dual-trap detection is always superior to that of more traditional, single-trap designs, despite the added Brownian noise of the second trapped microsphere... - Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torqueMarcelo Nollmann
Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
Nat Struct Mol Biol 14:264-71. 2007..A third mode is responsible for the ATP-independent relaxation of negative supercoils. We present a branched kinetic model that quantitatively accounts for all of our single-molecule results and agrees with existing biochemical data... - Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanismTimothy A Brown
Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
Genes Dev 19:2466-76. 2005..These data reconcile the original displacement mode of replication with the data obtained from 2D gel analyses... - Identification of the FtsK sequence-recognition domainJerod L Ptacin
Department of Molecular and Cell Biology, University of California, Berkeley, California 94720 3204, USA
Nat Struct Mol Biol 13:1023-5. 2006..Here, we use in vitro single-molecule and ensemble methods to unveil a mechanism of action in which the translocation and sequence-recognition activities are performed by different domains in FtsK... - Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging processLuis R Comolli
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Virology 371:267-77. 2008..Monte Carlo simulations of the packaging process provide insights on the forces involved and the resultant structures... - Mechanism of force generation of a viral DNA packaging motorYann R Chemla
Department of Physics, University of California, Berkeley, Berkeley, California 94720, USA
Cell 122:683-92. 2005..We also show that the motor subunits act in a coordinated, successive fashion with high processivity. Finally, we propose a minimal mechanochemical cycle of this DNA-translocating ATPase that rationalizes all of our findings... - Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurementsJeff Gore
Department of Physics, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 100:12564-9. 2003..The Jarzynski-estimator bias is shown to be the dominant source of error in many cases. Our expression for the bias is used to develop a bias-corrected Jarzynski free-energy difference estimator in the near-equilibrium regime... - The folding cooperativity of a protein is controlled by its chain topologyElizabeth A Shank
Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
Nature 465:637-40. 2010..We speculate that proteins may have evolved to select certain topologies that increase coupling between regions to avoid areas of the landscape that lead to kinetic trapping and misfolding... - Temperature control methods in a laser tweezers systemHanbin Mao
Lawrence Berkeley National Laboratory, California 94720, USA
Biophys J 89:1308-16. 2005..The utility of the second method was demonstrated in single-molecule experiments by measuring the mechanical stretch of a 41 kbp lambda double-stranded DNA at temperatures ranging from 8.4 degrees C to 45.6 degrees C... - Differential force microscope for long time-scale biophysical measurementsJason L Choy
Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA
Rev Sci Instrum 78:043711. 2007.... - Light-powering Escherichia coli with proteorhodopsinJessica M Walter
Department of Physics, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 104:2408-12. 2007..Proteorhodopsin allows Escherichia coli cells to withstand environmental respiration challenges by harvesting light energy... - Analysis of P element transposase protein-DNA interactions during the early stages of transpositionMei Tang
Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
J Biol Chem 282:29002-12. 2007.... - Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocaseOren Levy
Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 102:17618-23. 2005..Finally, we show that the FtsK translocase is a powerful motor that is able to displace a triplex-forming oligo from a DNA substrate... - Laminin and biomimetic extracellular elasticity enhance functional differentiation in mammary epitheliaJordi Alcaraz
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
EMBO J 27:2829-38. 2008..Our data indicate that tissue-specific gene expression is controlled by both the tissues' unique biochemical milieu and mechanical properties, processes involved in maintenance of tissue integrity and protection against tumorigenesis... - Exact solutions for kinetic models of macromolecular dynamicsYann R Chemla
Department of Physics, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
J Phys Chem B 112:6025-44. 2008..Furthermore, we show that this formalism allows calculation of these parameters for a much wider class of general kinetic models than demonstrated with previous methods...
Research Grants
- Mechanisms of Viral DNA PackagingCARLOS JOSE BUSTAMANTE; Fiscal Year: 2010..Finally, we wish to investigate how the increasing internal DNA pressure regulates the dynamics of the motor during packaging. ..
- PHYSICAL CHEMISTRY OF NUCLEIC ACIDSCarlos Bustamante; Fiscal Year: 2007..Finally, in the experiments described here, mechanical force will be used as a new controllable variable to characterize the process of mechanochemical transduction in this motor enzyme. ..
- Mechanisms of Viral DNA PackagingCarlos Bustamante; Fiscal Year: 2007..These studies will shed light on fundamental principles of protein-nucleic acid and protein-protein interactions, macromolecular self-assembly and conformational change, and mechanochemical energy transduction. ..
- PHYSICAL CHEMISTRY OF NUCLEIC ACIDSCARLOS JOSE BUSTAMANTE; Fiscal Year: 2010..The insights that our experiments provide on transcription will support the first steps in the development of future therapies. ..