Professional Education

  • Bachelor of Science, University of California Berkeley (2008)
  • Doctor of Philosophy, Massachusetts Institute of Technology (2014)

Stanford Advisors

All Publications

  • Single upconversion nanoparticle imaging at sub-10 W cm(-2) irradiance NATURE PHOTONICS Liu, Q., Zhang, Y., Peng, C., Yang, T., Joubert, L., Chu, S. 2018; 12 (9): 548–53
  • Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity. Proceedings of the National Academy of Sciences of the United States of America Peng, C. S., Fedeles, B. I., Singh, V., Li, D., Amariuta, T., Essigmann, J. M., Tokmakoff, A. 2015; 112 (11): 3229–34


    Antiviral drugs designed to accelerate viral mutation rates can drive a viral population to extinction in a process called lethal mutagenesis. One such molecule is 5,6-dihydro-5-aza-2'-deoxycytidine (KP1212), a selective mutagen that induces A-to-G and G-to-A mutations in the genome of replicating HIV. The mutagenic property of KP1212 was hypothesized to originate from its amino-imino tautomerism, which would explain its ability to base pair with either G or A. To test the multiple tautomer hypothesis, we used 2D IR spectroscopy, which offers subpicosecond time resolution and structural sensitivity to distinguish among rapidly interconverting tautomers. We identified several KP1212 tautomers and found that >60% of neutral KP1212 is present in the enol-imino form. The abundant proportion of this traditionally rare tautomer offers a compelling structure-based mechanism for pairing with adenine. Additionally, the pKa of KP1212 was measured to be 7.0, meaning a substantial population of KP1212 is protonated at physiological pH. Furthermore, the mutagenicity of KP1212 was found to increase dramatically at pH <7, suggesting a significant biological role for the protonated KP1212 molecules. Overall, our data reveal that the bimodal mutagenic properties of KP1212 result from its unique shape shifting ability that utilizes both tautomerization and protonation.

    View details for DOI 10.1073/pnas.1415974112

    View details for PubMedID 25733867

    View details for PubMedCentralID PMC4371980

  • Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America Peng, C. S., Baiz, C. R., Tokmakoff, A. 2013; 110 (23): 9243–48


    We provide a systematic characterization of the nanosecond ground-state lactam-lactim tautomerization of pyridone derivatives in aqueous solution under ambient conditions using temperature-jump transient 2D IR spectroscopy. Although electronic excited-state tautomerization has been widely studied, experimental work on the ground electronic state, most relevant to chemistry and biology, is lacking. Using 2D IR spectroscopy, lactam and lactim tautomers of 6-chloro-2-pyridone and 2-chloro-4-pyridone are unambiguously identified by their unique cross-peak patterns. Monitoring the correlated exponential relaxation of these signals in response to a laser temperature jump provides a direct measurement of the nanosecond tautomerization kinetics. By studying the temperature, concentration, solvent, and pH dependence, we extract a thermodynamic and kinetic characterization and conclude that the tautomerization proceeds through a two-state concerted mechanism. We find that the intramolecular proton transfer is mediated by bridging water molecules and the reaction barrier is dictated by the release of a proton from pyridone, as would be expected for an efficient Grothuss-type proton transfer mechanism.

    View details for DOI 10.1073/pnas.1303235110

    View details for PubMedID 23690588

    View details for PubMedCentralID PMC3677484

  • Anharmonic vibrational modes of nucleic acid bases revealed by 2D IR spectroscopy. Journal of the American Chemical Society Peng, C. S., Jones, K. C., Tokmakoff, A. 2011; 133 (39): 15650–60


    Polarization-dependent two-dimensional infrared (2D IR) spectra of the purine and pyrimadine base vibrations of five nucleotide monophosphates (NMPs) were acquired in D(2)O at neutral pH in the frequency range 1500-1700 cm(-1). The distinctive cross-peaks between the ring deformations and carbonyl stretches of NMPs indicate that these vibrational modes are highly coupled, in contrast with the traditional peak assignment, which is based on a simple local mode picture such as C═O, C═N, and C═C double bond stretches. A model of multiple anharmonically coupled oscillators was employed to characterize the transition energies, vibrational anharmonicities and couplings, and transition dipole strengths and orientations. No simple or intuitive structural correlations are found to readily assign the spectral features, except in the case of guanine and cytosine, which contain a single local CO stretching mode. To help interpret the nature of these vibrational modes, we performed density functional theory (DFT) calculations and found that multiple ring vibrations are coupled and delocalized over the purine and pyrimidine rings. Generally, there is close correspondence between the experimental and computational results, provided that the DFT calculations include explicit waters solvating hydrogen-bonding sites. These results provide direct experimental evidence of the delocalized nature of the nucleotide base vibrations via a nonperturbative fashion and will serve as building blocks for constructing a structure-based model of DNA and RNA vibrational spectroscopy.

    View details for DOI 10.1021/ja205636h

    View details for PubMedID 21861514

  • Studying Protein-Protein Binding through T-Jump Induced Dissociation: Transient 2D IR Spectroscopy of Insulin Dimer JOURNAL OF PHYSICAL CHEMISTRY B Zhang, X., Jones, K. C., Fitzpatrick, A., Peng, C. S., Feng, C., Baiz, C. R., Tokmakoff, A. 2016; 120 (23): 5134-5145


    Insulin homodimer associates through the coupled folding and binding of two partially disordered monomers. We aim to understand this dynamics by observing insulin dimer dissociation initiated with a nanosecond temperature jump using transient two-dimensional infrared spectroscopy (2D IR) of amide I vibrations. With the help of equilibrium FTIR and 2D IR spectra, and through a systematic study of the dependence of dissociation kinetics on temperature and insulin concentration, we are able to decompose and analyze the spectral evolution associated with different secondary structures. We find that the dissociation under all conditions is characterized by two processes whose influence on the kinetics varies with temperature: the unfolding of the β sheet at the dimer interface observed as exponential kinetics between 250 and 1000 μs and nonexponential kinetics between 5 and 150 μs that we attribute to monomer disordering. Microscopic reversibility arguments lead us to conclude that dimer association requires significant conformational changes within the monomer in concert with the folding of the interfacial β sheet. While our data indicates a more complex kinetics, we apply a two-state model to the β-sheet unfolding kinetics to extract thermodynamic parameters and kinetic rate constants. The association rate constant, ka (23 °C) = 8.8 × 10(5) M(-1) s(-1) (pH 0, 20% EtOD), is approximately 3 orders of magnitude slower than the calculated diffusion limited association rate, which is explained by the significant destabilizing effect of ethanol on the dimer state and the highly positive charge of the monomers at this pH.

    View details for DOI 10.1021/acs.jpcb.6b03246

    View details for Web of Science ID 000378194900004

    View details for PubMedID 27203447

  • Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing Stability. ACS chemical biology Dai, Q., Sanstead, P. J., Peng, C. S., Han, D., He, C., Tokmakoff, A. 2016; 11 (2): 470–77


    In the active cytosine demethylation pathway, 5-methylcytosine (5mC) is oxidized sequentially to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Thymine DNA glycosylase (TDG) selectively excises 5fC and 5caC but not cytosine (C), 5mC, and 5hmC. We propose that the electron-withdrawing properties of -CHO and -COOH in 5fC and 5caC increase N3 acidity, leading to weakened hydrogen bonding and reduced base pair stability relative to C, 5mC, and 5hmC, thereby facilitating the selective recognition of 5fC and 5caC by TDG. Through (13)C NMR, we measured the pKa at N3 of 5fC as 2.4 and the two pKa's of 5caC as 2.1 and 4.2. We used isotope-edited IR spectroscopy coupled with density functional theory (DFT) calculations to site-specifically assign the more acidic pKa of 5caC to protonation at N3, indicating that N3 acidity is increased in 5fC and 5caC relative to C. IR and UV melting studies of self-complementary DNA oligomers confirm reduced stability for 5fC-G and 5caC-G base pairs. Furthermore, while the 5fC-G base pair stability is insensitive to pH, the 5caC-G stability is reduced as pH decreases and the carboxyl group is increasingly protonated. Despite suggestions that 5fC and 5caC may exist in rare tautomeric structures which form wobble GC base pairs, our two-dimensional infrared (2D IR) spectroscopy of 5fC and 5caC free nucleosides confirms that both bases are predominantly in the canonical amino-keto form. Taken together, these findings support our model that weakened base pairing ability for 5fC and 5caC in dsDNA contributes to their selective recognition by TDG.

    View details for DOI 10.1021/acschembio.5b00762

    View details for PubMedID 26641274

    View details for PubMedCentralID PMC4782585

  • A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models. Biophysical journal Baiz, C. R., Lin, Y., Peng, C. S., Beauchamp, K. A., Voelz, V. A., Pande, V. S., Tokmakoff, A. 2014; 106 (6): 1359-1370


    The folding mechanism of the N-terminal domain of ribosomal protein L9 (NTL91-39) is studied using temperature-jump (T-jump) amide I' two-dimensional infrared (2D IR) spectroscopy in combination with spectral simulations based on a Markov state model (MSM) built from millisecond-long molecular dynamics trajectories. The results provide evidence for a compact well-structured folded state and a heterogeneous fast-exchanging denatured state ensemble exhibiting residual secondary structure. The folding rate of 26.4 μs(-1) (at 80°C), extracted from the T-jump response of NTL91-39, compares favorably with the 18 μs(-1) obtained from the MSM. Structural decomposition of the MSM and analysis along the folding coordinate indicates that helix-formation nucleates the global folding. Simulated difference spectra, corresponding to the global folding transition of the MSM, are in qualitative agreement with measured T-jump 2D IR spectra. The experiments demonstrate the use of T-jump 2D IR spectroscopy as a valuable tool for studying protein folding, with direct connections to simulations. The results suggest that in addition to predicting the correct native structure and folding time constant, molecular dynamics simulations carried out with modern force fields provide an accurate description of folding mechanisms in small proteins.

    View details for DOI 10.1016/j.bpj.2014.02.008

    View details for PubMedID 24655511

    View details for PubMedCentralID PMC3984984

  • Direct observation of multiple tautomers of oxythiamine and their recognition by the thiamine pyrophosphate riboswitch. ACS chemical biology Singh, V., Peng, C. S., Li, D., Mitra, K., Silvestre, K. J., Tokmakoff, A., Essigmann, J. M. 2014; 9 (1): 227–36


    Structural diversification of canonical nucleic acid bases and nucleotide analogues by tautomerism has been proposed to be a powerful on/off switching mechanism allowing regulation of many biological processes mediated by RNA enzymes and aptamers. Despite the suspected biological importance of tautomerism, attempts to observe minor tautomeric forms in nucleic acid or hybrid nucleic acid-ligand complexes have met with challenges due to the lack of sensitive methods. Here, a combination of spectroscopic, biochemical, and computational tools probed tautomerism in the context of an RNA aptamer-ligand complex; studies involved a model ligand, oxythiamine pyrophosphate (OxyTPP), bound to the thiamine pyrophosphate (TPP) riboswitch (an RNA aptamer) as well as its unbound nonphosphorylated form, oxythiamine (OxyT). OxyTPP, similarly to canonical heteroaromatic nucleic acid bases, has a pyrimidine ring that forms hydrogen bonding interactions with the riboswitch. Tautomerism was established using two-dimensional infrared (2D IR) spectroscopy, variable temperature FTIR and NMR spectroscopies, binding isotope effects (BIEs), and computational methods. All three possible tautomers of OxyT, including the minor enol tautomer, were directly identified, and their distributions were quantitated. In the bound form, BIE data suggested that OxyTPP existed as a 4'-keto tautomer that was likely protonated at the N1'-position. These results also provide a mechanistic framework for understanding the activation of riboswitch in response to deamination of the active form of vitamin B1 (or TPP). The combination of methods reported here revealing the fine details of tautomerism can be applied to other systems where the importance of tautomerism is suspected.

    View details for DOI 10.1021/cb400581f

    View details for PubMedID 24252063

    View details for PubMedCentralID PMC3956446

  • Tautomerism provides a molecular explanation for the mutagenic properties of the anti-HIV nucleoside 5-aza-5,6-dihydro-2'-deoxycytidine. Proceedings of the National Academy of Sciences of the United States of America Li, D., Fedeles, B. I., Singh, V., Peng, C. S., Silvestre, K. J., Simi, A. K., Simpson, J. H., Tokmakoff, A., Essigmann, J. M. 2014; 111 (32): E3252–9


    Viral lethal mutagenesis is a strategy whereby the innate immune system or mutagenic pool nucleotides increase the error rate of viral replication above the error catastrophe limit. Lethal mutagenesis has been proposed as a mechanism for several antiviral compounds, including the drug candidate 5-aza-5,6-dihydro-2'-deoxycytidine (KP1212), which causes A-to-G and G-to-A mutations in the HIV genome, both in tissue culture and in HIV positive patients undergoing KP1212 monotherapy. This work explored the molecular mechanism(s) underlying the mutagenicity of KP1212, and specifically whether tautomerism, a previously proposed hypothesis, could explain the biological consequences of this nucleoside analog. Establishing tautomerism of nucleic acid bases under physiological conditions has been challenging because of the lack of sensitive methods. This study investigated tautomerism using an array of spectroscopic, theoretical, and chemical biology approaches. Variable temperature NMR and 2D infrared spectroscopic methods demonstrated that KP1212 existed as a broad ensemble of interconverting tautomers, among which enolic forms dominated. The mutagenic properties of KP1212 were determined empirically by in vitro and in vivo replication of a single-stranded vector containing a single KP1212. It was found that KP1212 paired with both A (10%) and G (90%), which is in accord with clinical observations. Moreover, this mutation frequency is sufficient for pushing a viral population over its error catastrophe limit, as observed before in cell culture studies. Finally, a model is proposed that correlates the mutagenicity of KP1212 with its tautomeric distribution in solution.

    View details for DOI 10.1073/pnas.1405635111

    View details for PubMedID 25071207

    View details for PubMedCentralID PMC4136561

  • Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America Jones, K. C., Peng, C. S., Tokmakoff, A. 2013; 110 (8): 2828–33


    We provide a time- and structure-resolved characterization of the folding of the heterogeneous β-hairpin peptide Tryptophan Zipper 2 (Trpzip2) using 2D IR spectroscopy. The amide I' vibrations of three Trpzip2 isotopologues are used as a local probe of the midstrand contacts, β-turn, and overall β-sheet content. Our experiments distinguish between a folded state with a type I' β-turn and a misfolded state with a bulged turn, providing evidence for distinct conformations of the peptide backbone. Transient 2D IR spectroscopy at 45 °C following a laser temperature jump tracks the nanosecond and microsecond kinetics of unfolding and the exchange between conformers. Hydrogen bonds to the peptide backbone are loosened rapidly compared with the 5-ns temperature jump. Subsequently, all relaxation kinetics are characterized by an observed 1.2 ± 0.2-μs exponential. Our time-dependent 2D IR spectra are explained in terms of folding of either native or nonnative contacts from a common compact disordered state. Conversion from the disordered state to the folded state is consistent with a zip-out folding mechanism.

    View details for DOI 10.1073/pnas.1211968110

    View details for PubMedID 23382249

    View details for PubMedCentralID PMC3581973

  • Identification of Lactam-Lactim Tautomers of Aromatic Heterocycles in Aqueous Solution Using 2D IR Spectroscopy. The journal of physical chemistry letters Peng, C. S., Tokmakoff, A. 2012; 3 (22): 3302–6


    The tautomerism of aromatic heterocycles is of great interest because it directly affects their chemical properties and biological function. The tautomerism of 2-pyridone, 6-chloro-2-pyridone, and 4-pyrimidinone have been examined in D(2)O using FTIR, two-dimensional IR (2D IR) spectroscopy and density functional theory (DFT) calculations. Using the 2D IR cross-peak patterns, the lactim tautomer of 6-chloro-2-pyridone was separated from the lactam tautomer, and its population was observed to increase with temperature. The equilibrium constant of [lac-tam]/[lactim] was determined to be 2.1 at room temperature for 6-chloro-2-pyridone. Similarly, the N1H and N3H lactam tautomers of 4-pyrimidinone were identified with 2D IR. To assign the vibrational modes of different tautomers, DFT calculations of these chemical species were performed with explicit water molecules, and the hydration effects on the vibrational frequencies and intensities were established.

    View details for DOI 10.1021/jz301706a

    View details for PubMedID 23227298

    View details for PubMedCentralID PMC3516185

  • Coherent two-dimensional infrared spectroscopy: quantitative analysis of protein secondary structure in solution. The Analyst Baiz, C. R., Peng, C. S., Reppert, M. E., Jones, K. C., Tokmakoff, A. 2012; 137 (8): 1793–99


    We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent two-dimensional infrared (2DIR) spectroscopy of backbone amide I vibrations (1550-1720 cm(-1)). Sixteen proteins with known crystal structures were used to construct a library of 2DIR spectra, and the fraction of residues in α-helix, β-sheet, and unassigned conformations was determined by singular value decomposition (SVD) of the measured two-dimensional spectra. The method was benchmarked by removing each individual protein from the set and comparing the composition extracted from 2DIR against the composition determined from the crystal structures. To highlight the increased structural content extracted from 2DIR spectra a similar analysis was also carried out using conventional infrared absorption of the proteins in the library.

    View details for DOI 10.1039/c2an16031e

    View details for PubMedID 22398665

  • Ultrafast dynamics in helium nanodroplets probed by femtosecond time-resolved EUV photoelectron imaging. The journal of physical chemistry. A Kornilov, O., Wang, C. C., Bünermann, O., Healy, A. T., Leonard, M., Peng, C., Leone, S. R., Neumark, D. M., Gessner, O. 2010; 114 (3): 1437–45


    The dynamics of electronically excited helium nanodroplets are studied by femtosecond time-resolved photoelectron imaging. EUV excitation into a broad absorption band centered around 23.8 eV leads to an indirect photoemission process that generates ultraslow photoelectrons. A 1.58 eV probe pulse transiently depletes the indirect photoemission signal for pump-probe time delays <200 fs and enhances the signal beyond this delay. The depletion is due to suppression of the indirect ionization process by the probe photon, which generates a broad, isotropically emitted photoelectron band. Similar time scales in the decay of the high energy photoelectron signal and the enhancement of the indirect photoemission signal suggest an internal relaxation process that populates states in the range of a lower energy droplet absorption band located just below the droplet ionization potential (IP approximately 23.0 eV). A nearly 70% enhancement of the ultraslow photoelectron signal indicates that interband relaxation plays a more dominant role for the droplet de-excitation mechanism than photoemission.

    View details for DOI 10.1021/jp907312t

    View details for PubMedID 20043659

  • Melting of a beta-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations. The journal of physical chemistry. B Smith, A. W., Lessing, J., Ganim, Z., Peng, C. S., Tokmakoff, A., Roy, S., Jansen, T. L., Knoester, J. 2010; 114 (34): 10913–24


    Isotope-edited two-dimensional infrared spectroscopy has been used to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (TZ2) across its thermal unfolding transition. Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the beta-turn (K8), the N-terminus (S1), and the midstrand region (T10 and T3T10). Isotope-shifts, 2D lineshapes, and other spectral changes to the amide I 2D IR spectra of labeled TZ2 isotopologues were observed as a function of temperature. Data were interpreted on the basis of structure-based spectroscopic modeling of conformers obtained from extensive molecular dynamics simulations. The K8 spectra reveal two unique turn geometries, the type I' beta-turn observed in the NMR structure, and a less populated disordered or bulged loop. The data indicate that structures at low temperature resemble the folded NMR structure with typical cross-strand hydrogen bonds, although with a subpopulation of misformed turns. As the temperature is raised from 25 to 85 degrees C, the fraction of population with a type I' turn increases, but the termini also fray. Hydrogen bonding contacts in the midstrand region remain at all temperatures although with increasing thermal disorder. Our data show no evidence of an extended chain or random coil state for the TZ2 peptide at any temperature. The methods demonstrated here offer an approach to characterizing conformational variation within the folded or unfolded states of proteins and peptides.

    View details for DOI 10.1021/jp104017h

    View details for PubMedID 20690697