CARLOS JOSE BUSTAMANTE

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Intersubunit coordination in a homomeric ring ATPase
    Jeffrey 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
  2. pmc Substrate interactions and promiscuity in a viral DNA packaging motor
    K Aathavan
    Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
    Nature 461:669-73. 2009
  3. pmc The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes
    Lacramioara Bintu
    Jason L Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, Berkeley, California, USA
    Nat Struct Mol Biol 18:1394-9. 2011
  4. ncbi request reprint Unfolding single RNA molecules: bridging the gap between equilibrium and non-equilibrium statistical thermodynamics
    Carlos 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
  5. doi request reprint In singulo biochemistry: when less is more
    Carlos Bustamante
    Department of Physics and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Annu Rev Biochem 77:45-50. 2008
  6. ncbi request reprint Grabbing the cat by the tail: manipulating molecules one by one
    C Bustamante
    Howard Hughes Medical Institute, Berkeley, California, USA
    Nat Rev Mol Cell Biol 1:130-6. 2000
  7. pmc Of torques, forces, and protein machines
    Carlos Bustamante
    Department of Physics, University of California at Berkeley, Berkeley, CA 94720 7300, USA
    Protein Sci 13:3061-5. 2004
  8. ncbi request reprint Mechanical processes in biochemistry
    Carlos 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
  9. pmc Revisiting the central dogma one molecule at a time
    Carlos Bustamante
    Jason L Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, 94720, USA
    Cell 144:480-97. 2011
  10. ncbi request reprint Ten years of tension: single-molecule DNA mechanics
    Carlos Bustamante
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Nature 421:423-7. 2003

Research Grants

  1. Mechanisms of Viral DNA Packaging
    Carlos Bustamante; Fiscal Year: 2004
  2. Mechanisms of Viral DNA Packaging
    CARLOS JOSE BUSTAMANTE; Fiscal Year: 2010
  3. PHYSICAL CHEMISTRY OF NUCLEIC ACIDS
    Carlos Bustamante; Fiscal Year: 2007
  4. Mechanisms of Viral DNA Packaging
    Carlos Bustamante; Fiscal Year: 2007
  5. Mechanisms of Viral DNA Packaging
    Carlos Bustamante; Fiscal Year: 2006
  6. Mechanisms of Viral DNA Packaging
    Carlos Bustamante; Fiscal Year: 2005
  7. PHYSICAL CHEMISTRY OF NUCLEIC ACIDS
    Carlos Bustamante; Fiscal Year: 2009
  8. PHYSICAL CHEMISTRY OF NUCLEIC ACIDS
    CARLOS JOSE BUSTAMANTE; Fiscal Year: 2010

Collaborators

Detail Information

Publications63

  1. pmc Intersubunit coordination in a homomeric ring ATPase
    Jeffrey 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...
  2. pmc Substrate interactions and promiscuity in a viral DNA packaging motor
    K 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...
  3. pmc The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes
    Lacramioara Bintu
    Jason L Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, Berkeley, California, USA
    Nat Struct Mol Biol 18:1394-9. 2011
    ..Factors affecting the relative magnitude of these processes provide the physical basis for nucleosomal fate during transcription and, therefore, for the regulation of gene expression...
  4. ncbi request reprint Unfolding single RNA molecules: bridging the gap between equilibrium and non-equilibrium statistical thermodynamics
    Carlos 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...
  5. doi request reprint In singulo biochemistry: when less is more
    Carlos 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...
  6. ncbi request reprint Grabbing the cat by the tail: manipulating molecules one by one
    C 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...
  7. pmc Of torques, forces, and protein machines
    Carlos Bustamante
    Department of Physics, University of California at Berkeley, Berkeley, CA 94720 7300, USA
    Protein Sci 13:3061-5. 2004
  8. ncbi request reprint Mechanical processes in biochemistry
    Carlos 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...
  9. pmc Revisiting the central dogma one molecule at a time
    Carlos 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...
  10. ncbi request reprint Ten years of tension: single-molecule DNA mechanics
    Carlos 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...
  11. pmc Determination of thermodynamics and kinetics of RNA reactions by force
    Ignacio 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...
  12. pmc Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results
    Jin 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...
  13. pmc Proofreading dynamics of a processive DNA polymerase
    Borja 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...
  14. ncbi request reprint DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC
    Yongli 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...
  15. ncbi request reprint Characterization of the mechanical unfolding of RNA pseudoknots
    Lisa 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...
  16. ncbi request reprint Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
    Jan 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...
  17. pmc Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method
    Andres 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...
  18. pmc Measurement of the effect of monovalent cations on RNA hairpin stability
    Jeffrey 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...
  19. pmc Molecular handles for the mechanical manipulation of single-membrane proteins in living cells
    Pau 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...
  20. pmc RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP
    Sophie 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...
  21. doi request reprint Recent advances in optical tweezers
    Jeffrey 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...
  22. pmc Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods
    Pan 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...
  23. doi request reprint Coupling translocation with nucleic acid unwinding by NS3 helicase
    Jin 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...
  24. pmc Protein-DNA chimeras for single molecule mechanical folding studies with the optical tweezers
    Ciro 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...
  25. pmc NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening fork
    Wei 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...
  26. pmc Real-time control of the energy landscape by force directs the folding of RNA molecules
    Pan 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...
  27. ncbi request reprint Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding
    Eric 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
    ....
  28. pmc Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II
    Courtney 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...
  29. ncbi request reprint DNA overwinds when stretched
    Jeff 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...
  30. pmc Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations
    Jeffrey R Moffitt
    Department of Physics, University of California, Berkeley, 94720, USA
    Proc Natl Acad Sci U S A 107:15739-44. 2010
    ....
  31. pmc Guanosine triphosphate acts as a cofactor to promote assembly of initial P-element transposase-DNA synaptic complexes
    Mei 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...
  32. ncbi request reprint The bacterial condensin MukBEF compacts DNA into a repetitive, stable structure
    Ryan 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...
  33. pmc Mechanochemical analysis of DNA gyrase using rotor bead tracking
    Jeff Gore
    Department of Physics, University of California, Berkeley, California 94720, USA
    Nature 439:100-4. 2006
    ....
  34. ncbi request reprint Sequence-directed DNA translocation by purified FtsK
    Paul 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...
  35. pmc Effect of force on mononucleosomal dynamics
    Shirley 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...
  36. ncbi request reprint Structural transitions and elasticity from torque measurements on DNA
    Zev 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...
  37. pmc Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases
    Michael 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...
  38. pmc Unusual mechanical stability of a minimal RNA kissing complex
    Pan 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...
  39. pmc Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting
    Gang 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...
  40. pmc Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements
    Jeff 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...
  41. ncbi request reprint Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque
    Marcelo 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...
  42. ncbi request reprint Mechanochemistry of a viral DNA packaging motor
    Jin 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...
  43. doi request reprint Methods in statistical kinetics
    Jeffrey 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...
  44. ncbi request reprint The effect of force on thermodynamics and kinetics of single molecule reactions
    Ignacio 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...
  45. pmc Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase
    Nancy 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
    ....
  46. ncbi request reprint Mechanism of force generation of a viral DNA packaging motor
    Yann 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...
  47. pmc Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism
    Timothy 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...
  48. pmc Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis
    Jerod 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
    ....
  49. ncbi request reprint Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner
    Eric 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...
  50. ncbi request reprint Identification of the FtsK sequence-recognition domain
    Jerod 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...
  51. ncbi request reprint Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process
    Luis 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...
  52. pmc Differential detection of dual traps improves the spatial resolution of optical tweezers
    Jeffrey 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...
  53. pmc Thermal probing of E. coli RNA polymerase off-pathway mechanisms
    Yara 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...
  54. pmc Following translation by single ribosomes one codon at a time
    Jin 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...
  55. pmc Light-powering Escherichia coli with proteorhodopsin
    Jessica 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...
  56. pmc Laminin and biomimetic extracellular elasticity enhance functional differentiation in mammary epithelia
    Jordi 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...
  57. pmc Differential force microscope for long time-scale biophysical measurements
    Jason L Choy
    Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA
    Rev Sci Instrum 78:043711. 2007
    ....
  58. ncbi request reprint Analysis of P element transposase protein-DNA interactions during the early stages of transposition
    Mei 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
    ....
  59. doi request reprint Exact solutions for kinetic models of macromolecular dynamics
    Yann 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...
  60. pmc The folding cooperativity of a protein is controlled by its chain topology
    Elizabeth 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...
  61. pmc Temperature control methods in a laser tweezers system
    Hanbin 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...
  62. pmc Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase
    Oren 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...

Research Grants10

  1. Mechanisms of Viral DNA Packaging
    Carlos Bustamante; Fiscal Year: 2004
    ..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. ..
  2. Mechanisms of Viral DNA Packaging
    CARLOS JOSE BUSTAMANTE; Fiscal Year: 2010
    ..Finally, we wish to investigate how the increasing internal DNA pressure regulates the dynamics of the motor during packaging. ..
  3. PHYSICAL CHEMISTRY OF NUCLEIC ACIDS
    Carlos 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. ..
  4. Mechanisms of Viral DNA Packaging
    Carlos 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. ..
  5. Mechanisms of Viral DNA Packaging
    Carlos Bustamante; Fiscal Year: 2006
    ..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. ..
  6. Mechanisms of Viral DNA Packaging
    Carlos Bustamante; Fiscal Year: 2005
    ..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. ..
  7. PHYSICAL CHEMISTRY OF NUCLEIC ACIDS
    Carlos Bustamante; Fiscal Year: 2009
    ..The insights that our experiments provide on transcription will support the first steps in the development of future therapies. ..
  8. PHYSICAL CHEMISTRY OF NUCLEIC ACIDS
    CARLOS JOSE BUSTAMANTE; Fiscal Year: 2010
    ..The insights that our experiments provide on transcription will support the first steps in the development of future therapies. ..