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Carlos Bustamante

Bio: Carlos Bustamante is an academic researcher from Stanford University. The author has contributed to research in topics: Population & Optical tweezers. The author has an hindex of 161, co-authored 770 publications receiving 106053 citations. Previous affiliations of Carlos Bustamante include Lawrence Berkeley National Laboratory & University of California.


Papers
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Journal ArticleDOI
TL;DR: This research presents a meta-modelling architecture that automates the very labor-intensive and therefore time-heavy and expensive and therefore expensive and expensive process of designing and implementing nanofiltration systems.
Abstract: volume 30 number 3 march 2012 nature biotechnology Liege, Belgium. 31The Babraham Institute, Cambridge, UK. 32Genomatix Software GmbH, Munich, Germany. 33Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. 34Christian-Albrechts-Universitaet Zu Kiel, Kiel, Germany. 35Cellzome AG, Heidelberg, Germany. 36Institut National de la Sante et de la Recherche Medicale, Marseille, France. 37Weizmann Institute of Science, Rehovot, Israel. 38Barcelona Supercomputing Center, Barcelona, Spain. 39Centro Nacional de Investigaciones Oncologicas, Madrid, Spain. 40University Medical Centre Groningen, Groningen, The Netherlands. 41University of Saarland, Saarbruecken, Germany. 42Oxford Nanopore Technologies Ltd., Oxford, UK. e-mail: h.stunnenberg@ncmls.ru.nl

121 citations

08 Jan 2015
TL;DR: In this article, the authors used single-molecule fluorescence correlation spectroscopy to show that for enzymes that catalyse chemical reactions with large reaction enthalpies, the heat released at the protein's active site during catalysis transiently displaces the protein center-of-mass, essentially giving rise to a recoil effect that propels the enzyme.
Abstract: It has been traditionally assumed that the heat released during a single enzymatic catalytic event does not perturb the enzyme in any way; however, here single-molecule fluorescence correlation spectroscopy is used to show that, for enzymes that catalyse chemical reactions with large reaction enthalpies, the heat released at the protein's active site during catalysis transiently displaces the protein's centre-of-mass, essentially giving rise to a recoil effect that propels the enzyme. Enzymes catalyse chemical transformations by lowering the activation energy of those reactions. It is traditionally assumed that the heat released during a single catalytic event (a 'turnover' event) does not perturb the enzyme in any way. In this manuscript, the authors used single-molecule fluorescence correlation spectroscopy to show that for enzymes that catalyse chemical reactions with large reaction enthalpies (for example, catalase or alkaline phosphatase), the heat released at the protein's active site during catalysis transiently displaces the protein's centre-of-mass, essentially giving rise to a recoil effect that propels the enzyme. This work helps explain the recent finding that the diffusivity of enzymes increases in a substrate-dependent manner during catalysis. Recent studies have shown that the diffusivity of enzymes increases in a substrate-dependent manner during catalysis1,2. Although this observation has been reported and characterized for several different systems3,4,5,6,7,8,9,10, the precise origin of this phenomenon is unknown. Calorimetric methods are often used to determine enthalpies from enzyme-catalysed reactions and can therefore provide important insight into their reaction mechanisms11,12. The ensemble averages involved in traditional bulk calorimetry cannot probe the transient effects that the energy exchanged in a reaction may have on the catalyst. Here we obtain single-molecule fluorescence correlation spectroscopy data and analyse them within the framework of a stochastic theory to demonstrate a mechanistic link between the enhanced diffusion of a single enzyme molecule and the heat released in the reaction. We propose that the heat released during catalysis generates an asymmetric pressure wave that results in a differential stress at the protein–solvent interface that transiently displaces the centre-of-mass of the enzyme (chemoacoustic effect). This novel perspective on how enzymes respond to the energy released during catalysis suggests a possible effect of the heat of reaction on the structural integrity and internal degrees of freedom of the enzyme.

121 citations

Journal ArticleDOI
TL;DR: GNGNAGGG, its complement, or both are identified as a sequence motif that controls translocation directionality and it is shown that the FtsK translocase is a powerful motor that is able to displace a triplex-forming oligo from a DNA substrate.
Abstract: FtsK from Escherichia coli is a fast and sequence-directed DNA translocase with roles in chromosome dimer resolution, segregation, and decatenation. From the movement of single FtsK particles on defined DNA substrates and an analysis of skewed DNA sequences in bacteria, we identify GNGNAGGG, its complement, or both as a sequence motif that controls translocation directionality. GNGNAGGG is skewed so that it is predominantly on the leading strand of chromosomal replication. Translocation across this octamer from the 3′ side of the G-rich strand causes FtsK to pause, turn around, and translocate in the opposite direction. Only 39 ± 4% of the encounters between FtsK and the octamer result in a turnaround, congruent with our optimum turnaround probability prediction of 30%. The probability that the observed skew of GNGNAGGG within 1 megabase of dif occurred by chance in E. coli is 1.7 × 10–57, and similarly dramatic skews are found in the five other bacterial genomes we examined. The fact that FtsK acts only in the terminus region and the octamer skew extends from origin to terminus implies that this skew is also important in other basic cellular processes that are common among bacteria. Finally, we show that the FtsK translocase is a powerful motor that is able to displace a triplex-forming oligo from a DNA substrate.

120 citations

Journal ArticleDOI
24 Sep 2013-eLife
TL;DR: Surprisingly, it is found that the forward translocation rate is comparable to the catalysis rate, revealing a linear, non-branched ratchet mechanism for the nucleotide addition cycle in which translocation is one of the rate-limiting steps.
Abstract: During transcription elongation, RNA polymerase has been assumed to attain equilibrium between pre- and post-translocated states rapidly relative to the subsequent catalysis. Under this assumption, recent single-molecule studies proposed a branched Brownian ratchet mechanism that necessitates a putative secondary nucleotide binding site on the enzyme. By challenging individual yeast RNA polymerase II with a nucleosomal barrier, we separately measured the forward and reverse translocation rates. Surprisingly, we found that the forward translocation rate is comparable to the catalysis rate. This finding reveals a linear, non-branched ratchet mechanism for the nucleotide addition cycle in which translocation is one of the rate-limiting steps. We further determined all the major on- and off-pathway kinetic parameters in the elongation cycle. The resulting translocation energy landscape shows that the off-pathway states are favored thermodynamically but not kinetically over the on-pathway states, conferring the enzyme its propensity to pause and furnishing the physical basis for transcriptional regulation. DOI:http://dx.doi.org/10.7554/eLife.00971.001.

120 citations

Journal ArticleDOI
TL;DR: The results support models in which the F0 complex contains a ring of 9–12 c subunits with the b subunits located outside this ring, and show that scanning force microscopy is able to provide structural information on membrane proteins of molecular mass less than 200 000 Da.

120 citations


Cited by
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28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

14,558 citations

Journal ArticleDOI
Adam Auton1, Gonçalo R. Abecasis2, David Altshuler3, Richard Durbin4  +514 moreInstitutions (90)
01 Oct 2015-Nature
TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

12,661 citations

Journal Article
Fumio Tajima1
30 Oct 1989-Genomics
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

11,521 citations