About

Carlos Bustamante is a Professor of Biochemistry, Biophysics and Structural Biology at the University of California, Berkeley. He holds the Raymond and Beverly Sackler Chair and is an Investigator at the Howard Hughes Medical Institute. His research focuses on biochemistry and biophysics, with particular emphasis on molecular and cellular biology. He is associated with the Bustamante Lab located at 608A Stanley Hall, Berkeley, CA. His contact information includes email at carlosb@berkeley.edu, phone at (510) 666-2759, and mailing address at 176 Stanley Hall, University of California, Berkeley. Further details about his research can be found on his faculty webpage.

Research topics

• Physics
• Nanotechnology
• Computer Science
• Biology
• Materials science
• Engineering
• Chemistry
• Optics
• Biochemistry
• Biophysics
• Mechanical engineering
• Biological system

Selected publications

• The Central Coupler of the AAA+ ATPase ClpXP Controls Intersubunit Communication and Couples the Conversion of Chemical Energy into the Generation of Force

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-11 · 1 citations

  articleOpen accessSenior author

  ABSTRACT ClpX is a clockwise hexameric helical arrangement that hydrolyzes ATP to unfold proteins and translocate them into the proteolytic chamber. We investigate the central coupler, a three α-helix module conserved among AAA+ ATPases, which is proposed to enable intersubunit communication and mechanochemical coupling. Although fundamental in AAA+ ATPases, the molecular mechanism underlying these processes remains elusive in ClpX. By combining single-molecule optical tweezers, biochemical assays and single particle cryo-EM we demonstrate that the central coupler, of the second-highest subunit of the ClpX clockwise helical arrangement, positions its Arginine-finger, sensor-I and sensor-II to contact the ATP of the anticlockwise neighbor subunit to trigger its hydrolysis. Then, the central coupler of the highest subunit rapidly couples the ATP hydrolysis with the downward motion of its substrate-translocating loop, enabling fast force generation to swiftly unfold protein substrates while maximizing the thermodynamic efficiency of the motor.

  PublisherDOI

• Watching Alkaline Phosphatase Catalysis Through Its Vibrational Fingerprint

  Preprints.org · 2025-11-28

  preprintOpen access

  Despite decades of structural and kinetic characterization, the full spectral molecular vibrations that accompany the catalysis in alkaline phosphatase (ALP) have remained largely unexplored. In this study, we combine in situ real-time attenuated total reflection Fourier-transform infrared (ATR-FTIR) measurements over a large energy range, to track the hydrolysis of p-nitrophenyl phosphate (PNPP) and inorganic phosphate (Pi) over a large range of enzyme concentrations. From the static spectra of the pure components (ALP, PNPP, PNP, Pi), we identify their characteristic vibrational frequencies and use them as reference points for the time resolved spectra. The reaction reveals a monotonic growth of the inorganic-phosphate band at 1077 cm−1. At the highest alkaline-phosphatase concentration, we resolve two blue shifts in the nitro/aromatic region (1510 → 1518 cm−1; 1494 → 1499 cm−1), two red shifts in the fingerprint region (1345 → 1340 cm−1; 1294 → 1290 cm−1), and a splitting of the ~1592 cm−1 band into 1595 and 1583 cm−1. In conclusion, by anchoring the time-resolved spectra to the static spectra of individual constituents, we were able to resolve the infrared readout of the enzymatic reaction, offering a generalizable approach for FTIR-based tracking of catalytic processes.

  PublisherOA PDFDOI

• Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin

  Nature Cell Biology · 2025-09-30 · 1 citations

  articleOpen access

  How the facilitates chromatin transcription (FACT) complex enables RNA polymerase II to overcome chromatin barriers in cells remains poorly understood-especially given the limited direct interactions of FACT with polymerases, DNA or nucleosomes. Here we demonstrate that phase separation, mediated by nucleosome destabilizing factor (NDF), is a key mechanism enabling the function of FACT during transcription elongation. Through biochemical and single-molecule assays, we found that NDF-FACT condensates create specialized biochemical environments that enhance transcription efficiency approximately 20-fold compared with FACT alone. These dynamic condensates form on transcribing RNA polymerase II and travel along chromatin, where they promote efficient nucleosome disassembly at barriers while retaining histones on DNA to preserve chromatin integrity. In human stem cells, disruption of these condensates leads to genome-wide transcriptional defects and chromatin instability, mirroring the effects of FACT depletion. By showing that phase separation enhances FACT function during transcription elongation, our study reveals a key mechanism that preserves chromatin integrity and transcriptional homeostasis in human stem cells.

  PublisherOA PDFDOI

• Pleomorphic effects of three small-molecule inhibitors on transcription elongation by Mycobacterium tuberculosis RNA polymerase

  eLife · 2025-10-03

  articleOpen accessSenior author

  The Mycobacterium tuberculosis RNA polymerase (MtbRNAP) is the target of the first-line anti-tuberculosis inhibitor rifampin, however, the emergence of rifampin resistance necessitates the development of new antibiotics. Here, we communicate the first single-molecule characterization of MtbRNAP elongation and its inhibition by three diverse small-molecule inhibitors: N(α)-aroyl-N-aryl-phenylalaninamide (D-IX216), streptolydigin (Stl), and pseudouridimycin (PUM) using high-resolution optical tweezers. Compared to Escherichia coli RNA polymerase (EcoRNAP), MtbRNAP transcribes more slowly, has similar mechanical robustness, and only weakly recognizes E. coli pause sequences. The three small-molecule inhibitors of MtbRNAP exhibit strikingly different effects on transcription elongation. In the presence of D-IX216, which inhibits RNAP active-center bridge-helix motions required for nucleotide addition, the enzyme exhibits transitions between slowly and super-slowly elongating inhibited states. Stl, which inhibits the RNAP trigger-loop motions also required for nucleotide addition, inhibits RNAP primarily by inducing pausing and backtracking. PUM, a nucleoside analog of UTP, in addition to acting as a competitive inhibitor, induces the formation of slowly elongating RNAP inhibited states. Our results indicate that the three classes of small-molecule inhibitors affect the enzyme in distinct ways and show that the combination of Stl and D-IX216, which both target the RNAP bridge helix, has a strong synergistic effect on the enzyme.

  PublisherDOI

• Author response: Pleomorphic effects of three small-molecule inhibitors on transcription elongation by Mycobacterium tuberculosis RNA polymerase

  2025-08-15

  peer-reviewOpen accessSenior author
  PublisherDOI

• P310: Polygenic and rare variant contributions to the genetic architecture of familial hypercholesterolemia in a Mexican registry cohort

  Genetics in Medicine Open · 2025-01-01

  articleOpen access

  Introduction: Pharmacogenomics (PGx) is a rapidly developing field that utilizes an individual's genetic profile to establish a personalized medication treatment that best suits their genotype and variance in metabolism.PGx results can reactively or preemptively guide drug selection, dosing adjustment, and avoidance of certain medications and prevent adverse drug reactions (ADRs).A Pharmacogenomics Clinic (PGC) was established in January 2021 at Washington University School of Medicine (WUSM) to meet the expanding demands of PGx testing.The aims of this study were to examine the clinical utility and challenges of implementing PGx testing, determine the diagnostic yield, evaluate change of management, and propose guidelines for the selection of patients who will benefit from PGx testing.Methods: We conducted a retrospective chart review study of the first 100 patients evaluated at our PGC between January 2021 and November 2024.The study was approved by the WUSM Institutional Review Board.The majority of the patients in our cohort had PGx testing, which primarily comprised 25 pharmacogenes selected based on the availability of CPIC guidelines for their related variations.Patient data were extracted from electronic medical records, including demographic information, indications for testing, medication history, lack of insurance, and genetic results.Results: Two-thirds of the patients presented to the clinic were female and 94% of patients were referred from the outpatient setting.The mean age of patients was 26.2 years old (range: 1-79) and 90% identified as non-Hispanic White.The patients were mostly referred from genetics (48%), pediatrics (21%), and family medicine (19%).For patients who were referred to the PGC, the most frequent current diagnoses were anxiety (36%), depression (30%), migraine (20%), and constipation (20%).The most common currently used medications by patients were albuterol (27%), melatonin (23%), cetirizine (19%), and clonidine (17%), none of which have CPIC guidelines.Sertraline was the most often reported medication with ADRs (18%), followed by gabapentin, wellbutrin, guanfacine, and methylphenidate (16% each).Of the patients who presented to the PGC, 72% had never had prior PGx testing.The mean turnaround time for tests ordered by the PGx team was 27.6 days (range: 1 to 142 days).Analysis of PGx results revealed that all patients harbored at least one potentially actionable pharmacogenomic variant (mean: 5.6; range:1-9 per patient).The most frequently observed pharmacogenes with potentially actionable drug response phenotypes were: CYP2C19 (58%), UGT1A1 (57%), CYP2D6 (48%), and CYP2C9 (43%).Preliminary analysis, though incomplete, showed that PGx results led to patient management changes and improved medication selection outcomes.Conclusion: This study demonstrates the feasibility and clinical utility of PGx in a dedicated PGC.All patients in our cohort harbored at least one actionable variant in pharmacogenes including CYP2D6, CYP2C19, and CYP2C9 that are known to be involved in the metabolism of several mediation classes.Our findings suggest that PGx testing can inform medication management decisions and potentially improve patient outcomes.However, several challenges need to be addressed including long turnaround times for test results, high out-of-pocket costs, integrating PGx data into electronic health records, inclusion of underrepresented minorities, and lack of awareness of PGx testing availability.Further research is needed to establish comprehensive guidelines for patient selection and to fully evaluate the long-term impact of PGx-guided therapy on clinical outcomes and medication efficacy.

  PublisherOA PDFDOI

• Mercado de arriendo y vivienda social. La precarización de lo ya precarizado como acto iterativo territorial

  Papers Revista de Sociologia · 2025-10-31

  articleOpen accessSenior author

  En las últimas décadas, Chile ha experimentado un notable aumento en la tenencia de viviendas en arriendo y ha superado a otros países de América Latina. A través del estudio de las tipologías emergentes para arriendo en viviendas sociales, este artículo contribuye a comprender nuevas dinámicas relacionadas con la vivienda en alquiler y desarrolladas en el marco de la política habitacional chilena en la comuna de La Pintana, un territorio que fue clave en la producción de viviendas sociales destinadas a la propiedad de personas con bajos ingresos. El análisis del caso se basa en un estudio cualitativo y morfológico utilizando el concepto de bienestar basado en activos, lo que permitió comprender la inversión en alquiler como una forma de protección familiar frente a la incertidumbre, el riesgo y la precariedad, que se enfrentan de manera individual. Se propone que la transformación de la vivienda social representa una «precarización de lo ya precarizado», puesto que las nuevas morfologías para el alquiler resultan precarias, tanto para los inquilinos como también para los dueños que continúan habitando en estas viviendas de forma cada vez más jibarizada, en búsqueda de mayores rentabilidades.

  PublisherOA PDFDOI

• DNA origami–enhanced force spectroscopy and AlphaFold structural analyses reveal the folding landscape of calcium-binding proteins

  Science Advances · 2025-05-01 · 6 citations

  articleOpen accessSenior authorCorresponding

  Understanding the intricate folding process of proteins and characterizing the intermediates they populate en route to their native state remain challenging despite the remarkable accuracy achieved through in silico approaches for predicting native protein structures. Here, we replaced the conventional flexible double-stranded DNA handle force transducers with solid DNA-origami bundles to conduct single-molecule folding force-spectroscopy studies on calerythrin, a compact multidomain calcium-binding globular protein. The resulting origami-enhanced data revealed a previously "hidden" folding intermediate and the hierarchical nature of the protein's folding pathway. A systematic comparison of the AlphaFold-predicted conformational ensemble of structures of the native state and folding intermediates across various calcium-binding proteins provides a structural rationalization for the folding behavior of this protein family. The integration of DNA origami-enhanced single-molecule experiments with in silico approaches, and structural analysis presented here, constitutes a comprehensive method to uncover the rules underlying the formation of intermediates within protein folding landscapes.

  PublisherDOI

• Pleomorphic effects of three small-molecule inhibitors on transcription elongation by <i>Mycobacterium tuberculosis</i> RNA polymerase

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-07

  preprintOpen accessSenior authorCorresponding

  Abstract The Mycobacterium tuberculosis RNA polymerase (MtbRNAP) is the target of the first-line anti-tuberculosis inhibitor rifampin, however, the emergence of rifampin resistance necessitates the development of new antibiotics. Here, we communicate the first single-molecule characterization of MtbRNAP elongation and its inhibition by three diverse small-molecule inhibitors: N(α)-aroyl-N-aryl-phenylalaninamide (D-IX216), streptolydigin (Stl), and pseudouridimycin (PUM) using high-resolution optical tweezers. Compared to Escherichia coli RNA polymerase (EcoRNAP), MtbRNAP transcribes more slowly, has similar mechanical robustness, and only weakly recognizes E. coli pause sequences. The three small-molecule inhibitors of MtbRNAP exhibit strikingly different effects on transcription elongation. In the presence of D-IX216, which inhibits RNAP active-center bridge-helix motions required for nucleotide addition, the enzyme exhibits transitions between slowly and super-slowly elongating inhibited states. Stl, which inhibits the RNAP trigger-loop motions also required for nucleotide addition, inhibits RNAP primarily by inducing pausing and backtracking. PUM, a nucleoside analog of UTP, in addition to acting as a competitive inhibitor, induces the formation of slowly elongating RNAP inhibited states. Our results indicate that the three classes of small-molecule inhibitors affect the enzyme in distinct ways and show that the combination of Stl and D-IX216, which both target the RNAP bridge helix, has a strong synergistic effect on the enzyme.

  PublisherOA PDFDOI

• Watching Alkaline Phosphatase Catalysis Through Its Vibrational Fingerprint

  Biology · 2025-12-30

  articleOpen access

  Despite decades of structural and kinetic characterization, the full spectral molecular vibrations that accompany the catalysis in alkaline phosphatase (ALP) have remained largely unexplored. In this study, we combine in situ real-time attenuated total reflection Fourier transform infrared (ATR-FTIR) measurements over a large energy range to track the hydrolysis of p-nitrophenyl phosphate (PNPP) and inorganic phosphate (Pi) over a large range of enzyme concentrations. From the static spectra of the pure components (ALP, PNPP, PNP, Pi), we identify their characteristic vibrational frequencies and use them as reference points for the time-resolved spectra. The reaction reveals a monotonic growth of the inorganic-phosphate band at 1077 cm−1. At the highest alkaline phosphatase concentration, we resolve two blue shifts in the nitro/aromatic region (1510 → 1518 cm−1; 1494 → 1499 cm−1), two red shifts in the fingerprint region (1345 → 1340 cm−1; 1294 → 1290 cm−1), and a splitting of the ~1592 cm−1 band into 1595 and 1583 cm−1. In conclusion, by anchoring the time-resolved spectra to the static spectra of individual constituents, we were able to resolve the infrared readout of the enzymatic reaction, offering a generalizable approach for FTIR-based tracking of catalytic processes.

  PublisherDOI

Recent grants

• Mechanisms of Viral DNA Packaging

  NIH · $579k · 2018–2019

• NIH Grant R01GM071552

  NIH · $4.7M · 2017

• Physical Chemistry of Nucleic Acids

  NIH · $8.1M · 1983–2028

• Genetics and Developmental Biology Training Program

  NIH · $16.1M · 1979–2021

• NIH Grant R37GM032543

  NIH · $2.9M · 2009

Frequent coauthors

• Bibiana Onoa

  QB3

  116 shared

• Ignacio Tinoco

  University of California, Berkeley

  114 shared

• Steven B. Smith

  96 shared

• César Díaz-Celis

  University of California, Berkeley

  93 shared

• Eva Nogales

  Howard Hughes Medical Institute

  93 shared

• Ciro Cecconi

  83 shared

• Susan Marqusee

  QB3

  78 shared

• Shannon Yan

  78 shared

Education

• Ph.D., Human Biology

  University of California, Berkeley

  1996

• M.S., Human Biology

  University of California, Berkeley

  1993

• B.S., Molecular, Cellular, and Developmental Biology

  University of California, Santa Barbara

  1991

Awards & honors

• Howard Hughes Medical Institute Investigator
• Raymond and Beverly Sackler Chair