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Adhikary R, Zimmermann J, Stanfield RL, Wilson IA, Yu W, Oda M, Romesberg FE. Structure and Dynamics of Stacking Interactions in an Antibody Binding Site. Biochemistry 2019; 58:2987-2995. [PMID: 31243995 DOI: 10.1021/acs.biochem.9b00119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
For years, antibodies (Abs) have been used as a paradigm for understanding how protein structure contributes to molecular recognition. However, with the ability to evolve Abs that recognize specific chromophores, they also have great potential as models for how protein dynamics contribute to molecular recognition. We previously raised murine Abs to different chromophores and, with the use of three-pulse photon echo peak shift spectroscopy, demonstrated that the immune system is capable of producing Abs with widely varying flexibility. We now report the characterization of the complexes formed between two Abs, 5D11 and 10A6, and the chromophoric ligand that they were evolved to recognize, 8-methoxypyrene-1,3,6-trisulfonic acid (MPTS). The sequences of the Ab genes indicate that they evolved from a common precursor. We also used a variety of spectroscopic methods to probe the photophysics and dynamics of the Ab-MPTS complexes and found that they are similar to each other but distinct from previously characterized anti-MPTS Abs. Structural studies revealed that this difference likely results from a unique mode of binding in which MPTS is sandwiched between the side chain of PheH98, which interacts with the chromophore via T-stacking, and the side chain of TrpL91, which interacts with the chromophore via parallel stacking. The T-stacking interaction appears to mediate relaxation on the picosecond time scale, while the parallel stacking appears to mediate relaxation on an ultrafast, femtosecond time scale, which dominates the response. The anti-MPTS Abs thus not only demonstrate the simultaneous use of the two limiting modes of stacking for molecular recognition, but also provide a unique opportunity to characterize how dynamics might contribute to molecular recognition. Both types of stacking are common in proteins and protein complexes where they may similarly contribute to dynamics and molecular recognition.
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Affiliation(s)
| | | | | | | | | | - Masayuki Oda
- Graduate School of Life and Environmental Sciences , Kyoto Prefectural University , 1-5, Hangi-cho , Shimogamo, Sakyo-ku, Kyoto 606-8522 , Japan
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2
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Initial excited state structural dynamics of lumiflavin upon ultraviolet excitation. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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3
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Mondal S, Puranik M. Ultrafast Nuclear Dynamics of Photoexcited Guanosine-5'-Monophosphate in Three Singlet States. J Phys Chem B 2017; 121:7095-7107. [PMID: 28653848 DOI: 10.1021/acs.jpcb.7b05735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report measurement of resonance Raman (RR) spectra of guanosine-5'-monophosphate (GMP), a DNA nucleotide at excitation wavelengths throughout its ππ* absorption band (Bb) in the 210-230 nm range. From these data, we constructed wavelength-dependent Raman intensity excitation profiles (REPs) for all observed modes. These profiles and the absorption spectrum were then modeled using self-consistent simulations based on the time-dependent wave packet propagation formalism. We inferred the initial structural dynamics of GMP immediately after photoexcitation in terms of dimensionless displacements. The simulations also provide linewidth-broadening parameters that in turn report on the time scale of dynamics. We compared deduced structural changes in the purine ring upon photoabsorption into the Bb state with those deduced for the two lowest lying ππ* (La and Lb at 280 and 248 nm, respectively) excited states of GMP. We find that excitation to the Lb state lengthens C6-N1 and C2═N3 bonds, which lie along the formation coordinate of various oxidative adducts but Bb excitation does not. We also find that photoabsorption by the Bb state weakens the C8-N9 bond and thus might assist imidazole ring opening via cleavage of the same bond. Electronic excitation to different ππ* states of the guanine chromophore results in contrasting structural changes; although absorption by the La and Lb states induces expansion of pyrimidine and contraction of imidazole rings, excitation results in overall shrinkage of both the rings. Computed absolute changes in internal coordinates imply that photoexcitation to any of the three singlet states of GMP does not lead directly to the formation of a cation radical of guanine.
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Affiliation(s)
- Sayan Mondal
- Indian Institute of Science Education and Research , Pune 411008, India
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research , Pune 411008, India
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4
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Mondal S, Puranik M. Ultrafast structural dynamics of photoexcited adenine. Phys Chem Chem Phys 2017; 19:20224-20240. [DOI: 10.1039/c7cp03092d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ultraviolet Resonance Raman (UVRR) spectroscopy derives distinct electronic properties of adenine in the La (260 nm) and Bb (210 nm) excited states.
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Affiliation(s)
- Sayan Mondal
- Indian Institute of Science Education and Research
- Pune – 411008
- India
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research
- Pune – 411008
- India
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5
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Chi PB, Liberles DA. Selection on protein structure, interaction, and sequence. Protein Sci 2016; 25:1168-78. [PMID: 26808055 PMCID: PMC4918422 DOI: 10.1002/pro.2886] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 11/10/2022]
Abstract
Characterizing the probabilities of observing amino acid substitutions at specific sites in a protein over evolutionary time is a major goal in the field of molecular evolution. While purely statistical approaches at different levels of complexity exist, approaches rooted in underlying biological processes are necessary to characterize both the context-dependence of sequence changes (epistasis) and to extrapolate to sequences not observed in biological databases. To develop such approaches, an understanding of the different selective forces that act on amino acid substitution is necessary. Here, an overview of selection on and corresponding modeling of folding stability, folding specificity, binding affinity and specificity for ligands, the evolution of new binding sites on protein surfaces, protein dynamics, intrinsic disorder, and protein aggregation as well as the interplay with protein expression level (concentration) and biased mutational processes are presented.
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Affiliation(s)
- Peter B Chi
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122
- Department of Mathematics and Computer Science, Ursinus College, Collegeville, Pennsylvania, 19426
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122
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Adhikary R, Yu W, Oda M, Walker RC, Chen T, Stanfield RL, Wilson IA, Zimmermann J, Romesberg FE. Adaptive mutations alter antibody structure and dynamics during affinity maturation. Biochemistry 2015; 54:2085-93. [PMID: 25756188 PMCID: PMC5061043 DOI: 10.1021/bi501417q] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an example of adaptive evolution wherein the adaptive mutations may be identified and Abs may be raised to specific targets that facilitate the characterization of protein dynamics. Here, we report the characterization of three affinity matured Abs that evolved from a common germline precursor to bind the chromophoric antigen (Ag), 8-methoxypyrene-1,3,6-trisulfonate (MPTS). In addition to characterizing the sequence, molecular recognition, and structure of each Ab, we characterized the dynamics of each complex by determining their mechanical response to an applied force via three-pulse photon echo peak shift (3PEPS) spectroscopy and deconvoluting the response into elastic, anelastic, and plastic components. We find that for one Ab, affinity maturation was accomplished via the introduction of a single functional group that mediates a direct contact with MPTS and results in a complex with little anelasticity or plasticity. In the other two cases, more mutations were introduced but none directly contact MPTS, and while their effects on structure are subtle, their effects on anelasticity and plasticity are significant, with the level of plasticity correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation. A similar optimization of structure and dynamics may contribute to the evolution of other proteins.
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Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Wayne Yu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Ross C. Walker
- Department of Chemistry and Biochemistry, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Tingjian Chen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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7
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Milán-Garcés EA, Kaptan S, Puranik M. Mode-specific reorganization energies and ultrafast solvation dynamics of Tryptophan from Raman line-shape analysis. Biophys J 2014; 105:211-21. [PMID: 23823241 DOI: 10.1016/j.bpj.2013.04.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 10/26/2022] Open
Abstract
Tryptophan is widely used as an intrinsic fluorophore for studies of protein structure and dynamics. Its fluorescence is known to have two decay components with lifetimes of 0.5 and 3.1 ns. In this work we measure the ultrafast dynamics of Tryptophan at <100 fs through measurements and modeling of the Raman excitation profiles with time-dependent wave packet propagation theory. We use a Brownian oscillator model to simulate the water-tryptophan interaction. Upon photoexcitation to the higher singlet electronic state (Bb) the structure of tryptophan is distorted to an overall expansion of the pyrrole and benzene rings. The total reorganization energy for Trp in water is estimated to be 2169 cm(-1) with a 1230 cm(-1) contribution from the inertial response of water. The value of reorganization energy of water corresponding to the fast response is found to be higher than that obtained upon excitation to the La state by previous studies that used computational simulations. The long-time dynamics of Trp manifests as a conformational heterogeneity at shorter times and contributes to inhomogeneous broadening of the Raman profiles (315 cm(-1)).
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Affiliation(s)
- Erix A Milán-Garcés
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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8
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Adhikary R, Yu W, Oda M, Zimmermann J, Romesberg FE. Protein dynamics and the diversity of an antibody response. J Biol Chem 2012; 287:27139-47. [PMID: 22685303 PMCID: PMC3411056 DOI: 10.1074/jbc.m112.372698] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 05/25/2012] [Indexed: 01/08/2023] Open
Abstract
The immune system is remarkable in its ability to produce antibodies (Abs) with virtually any specificity from a limited repertoire of germ line precursors. Although the contribution of sequence diversity to this molecular recognition has been studied for decades, recent models suggest that protein dynamics may also broaden the range of targets recognized. To characterize the contribution of protein dynamics to immunological molecular recognition, we report the sequence, thermodynamic, and time-resolved spectroscopic characterization of a panel of eight Abs elicited to the chromophoric antigen 8-methoxypyrene-1,3,6-trisulfonate (MPTS). Based on the sequence data, three of the Abs arose from unique germ line Abs, whereas the remaining five comprise two sets of siblings that arose by somatic mutation of a common precursor. The thermodynamic data indicate that the Abs recognize MPTS via a variety of mechanisms. Although the spectroscopic data reveal small differences in protein dynamics, the anti-MPTS Abs generally show similar levels of flexibility and conformational heterogeneity, possibly representing the convergent evolution of the dynamics necessary for function. However, one Ab is significantly more rigid and conformationally homogeneous than the others, including a sibling Ab from which it differs by only five somatic mutations. This example of divergent evolution demonstrates that point mutations are capable of fixing significant differences in protein dynamics. The results provide unique insight into how high affinity Abs may be produced that bind virtually any target and possibly, from a more general perspective, how new protein functions are evolved.
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Affiliation(s)
- Ramkrishna Adhikary
- From the Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 and
| | - Wayne Yu
- From the Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 and
| | - Masayuki Oda
- the Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Jörg Zimmermann
- From the Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 and
| | - Floyd E. Romesberg
- From the Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 and
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9
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Nagasawa Y. Ultrafast photon echo experiments in condensed phase: Detection of solvation dynamics, coherent wavepacket motions and static inhomogeneity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2011. [DOI: 10.1016/j.jphotochemrev.2011.05.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Zimmermann J, Romesberg FE, Brooks CL, Thorpe IF. Molecular description of flexibility in an antibody combining site. J Phys Chem B 2010; 114:7359-70. [PMID: 20455589 PMCID: PMC2892760 DOI: 10.1021/jp906421v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mature antibodies (Abs) that are exquisitely specific for virtually any foreign molecule may be produced by affinity maturation of naïve (or germline) Abs. However, the finite number of germline Abs available suggests that, in contrast to mature Abs, germline Abs must be broadly polyspecific so that they are able to recognize a wide range of ligands. Thus, affinity maturation must play a role in mediating Ab specificity. One biophysical property that distinguishes polyspecificity from specificity is protein flexibility; a flexible combining site is able to adopt different conformations that recognize different foreign molecules (or antigens), while a rigid combining site is locked into a conformation that is specific for a given antigen. Recent studies (Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 8821-8826) have examined, at the atomic level, the structural properties that mediate changes in flexibility at four stages of affinity maturation in the 4-4-20 Ab. These studies employed molecular dynamics simulations to reveal a network of residue interactions that mediate the flexibility changes accompanying maturation. The flexibility of the Ab combining sites in these molecular systems was originally measured using three-pulse photon echo spectroscopy (3PEPS). The present investigation extends this work by providing a concrete link between structural properties of the Ab molecules and features of the spectroscopic measurements used to characterize their flexibility. Results obtained from the simulations are in good qualitative agreement with the experimental measurements and indicate that the spectroscopic signal is sensitive to protein dynamics distributed throughout the entire combining site. Thus, the simulations provide a molecular-level interpretation of the changes induced by affinity maturation of the Ab. The results suggest that 3PEPS spectroscopy in combination with molecular dynamics simulations can provide a detailed description of protein dynamics and, in this case, how it is evolved for biological function.
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Affiliation(s)
- Jörg Zimmermann
- Corresponding author. , Phone : (858) 784-7335, Fax : (858) 784-7472. , Phone: (410) 455-5728, Fax: (410) 455-2608
| | | | | | - Ian F. Thorpe
- Corresponding author. , Phone : (858) 784-7335, Fax : (858) 784-7472. , Phone: (410) 455-5728, Fax: (410) 455-2608
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11
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Bandaria JN, Cheatum CM, Kohen A. Examination of enzymatic H-tunneling through kinetics and dynamics. J Am Chem Soc 2009; 131:10151-5. [PMID: 19621965 DOI: 10.1021/ja902120t] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, kinetic measurements of isotope effects of enzyme-catalyzed reactions and their temperature dependence led to the development of theoretical models that were used to rationalize the findings. These models suggested that motions at the femto- to picosecond (fs to ps) time scale modulate the environment of the catalyzed reaction. Due to the fast nature of motions that directly affect the cleavage of a covalent bond, it is challenging to correlate the enzyme kinetics and dynamics related to that step. We report a study of formate dehydrogenase (FDH) that compares the temperature dependence of intrinsic kinetic isotope effects (KIEs) to measurements of the environmental dynamics at the fs-ps time scale (Bandaria et al. J. Am. Chem. Soc. 2008, 130, 22-23). The findings from this comparison of experimental kinetics and dynamics are consistent with models of environmentally coupled H-tunneling models, also known as Marcus-like models. Apparently, at tunneling ready conformations, the donor-acceptor distance, orientation, and fluctuations seems to be well tuned for H-transfer and are not affected by thermal fluctuations slower than 10 ps. This phenomenon has been suggested in the past to be quite general in enzymatic reactions. Here, the kinetics and the dynamics measurements on a single chemical step and on fs-ps time scale, respectively, provide new insight and support for the relevant theoretical models. Furthermore, this methodology could be applied to other systems and be used to examine mutants for which the organization of the donor and acceptor is not ideal, or enzymes with different rigidity and different temperature optimum.
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Affiliation(s)
- Jigar N Bandaria
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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12
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Jung G, Gerharz S, Schmitt A. Solvent-dependent steady-state fluorescence spectroscopy for searching ESPT-dyes: solvatochromism of HPTS revisited. Phys Chem Chem Phys 2009; 11:1416-26. [DOI: 10.1039/b816695a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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13
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Gibson EA, Shen Z, Jimenez R. Three-pulse photon echo peak shift spectroscopy as a probe of flexibility and conformational heterogeneity in protein folding. Chem Phys Lett 2009; 473:330-335. [PMID: 21103002 PMCID: PMC2983487 DOI: 10.1016/j.cplett.2009.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the equilibrium unfolding of Zn-cytochrome c in guanidine hydrochloride by three-pulse photon echo peak shift (3PEPS) spectroscopy. Unexpectedly, the measurements reveal that inhomogeneous broadening of the sample at the midpoint of the denaturation is larger than that of either native or unfolded states. To interpret this finding, we present simulations of the peak shift for both two-state and three-state unfolding models. Both the denaturant concentration dependence of the asymptotic peak shift (APS) and the wavelength dependence of the APS at the midpoint of the denaturation are different for the two models. Our data are consistent with two-state unfolding.
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Affiliation(s)
- Emily A. Gibson
- Department of Physics, University of Colorado Denver, Denver, CO 80217, USA
| | - Zhaochuan Shen
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
- Department of Physics, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Ralph Jimenez
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
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14
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Thielges MC, Zimmermann J, Yu W, Oda M, Romesberg FE. Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition. Biochemistry 2008; 47:7237-47. [PMID: 18549243 DOI: 10.1021/bi800374q] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The production of antibodies that selectively bind virtually any foreign compound is the hallmark of the immune system. While much is understood about how sequence diversity contributes to this remarkable feat of molecular recognition, little is known about how sequence diversity impacts antibody dynamics, which is also expected to contribute to molecular recognition. Toward this goal, we examined a panel of antibodies elicited to the chromophoric antigen fluorescein. On the basis of isothermal titration calorimetry, we selected six antibodies that bind fluorescein with diverse binding entropies, suggestive of varying contributions of dynamics to molecular recognition. Sequencing revealed that two pairs of antibodies employ homologous heavy chains that were derived from common germline genes, while the other two heavy chains and all six of the light chains were derived from different germline genes and are not homologous. Interestingly, more than half of all the somatic mutations acquired during affinity maturation among the six antibodies are located in positions unlikely to contact fluorescein directly. To quantify and compare the dynamics of the antibody-fluorescein complexes, three-pulse photon echo peak shift and transient grating spectroscopy were employed. All of the antibodies exhibited motions on three distinct time scales, ultrafast motions on the <100 fs time scale, diffusive motions on the picosecond time scale, and motions that occur on time scales longer than nanoseconds and thus appear static. However, the exact frequency of the picosecond time scale motion and the relative contribution of the different motions vary significantly among the antibody-chromophore complexes, revealing a high level of dynamic diversity. Using a hierarchical model, we relate the data to features of the antibodies' energy landscapes as well as their flexibility in terms of elasticity and plasticity. In all, the data provide a consistent picture of antibody flexibility, which interestingly appears to be correlated with binding entropy as well as with germline gene use and the mutations introduced during affinity maturation. The data also provide a gauge of the dynamic diversity of the antibody repertoire and suggest that this diversity might contribute to molecular recognition by facilitating the recognition of the broadest range of foreign molecules.
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Affiliation(s)
- Megan C Thielges
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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15
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Gilmore J, McKenzie RH. Quantum Dynamics of Electronic Excitations in Biomolecular Chromophores: Role of the Protein Environment and Solvent. J Phys Chem A 2008; 112:2162-76. [DOI: 10.1021/jp710243t] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Joel Gilmore
- Department of Physics, University of Queensland, Brisbane 4072 Australia
| | - Ross H. McKenzie
- Department of Physics, University of Queensland, Brisbane 4072 Australia
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16
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Gaudiosi DM, Gagnon E, Lytle AL, Fiore JL, Gibson EA, Kane S, Squier J, Murnane MM, Kapteyn HC, Jimenez R, Backus S. Multi-kilohertz repetition rate Ti:sapphire amplifier based on down-chirped pulse amplification. OPTICS EXPRESS 2006; 14:9277-9283. [PMID: 19529310 DOI: 10.1364/oe.14.009277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 08/04/2006] [Indexed: 05/27/2023]
Abstract
We present a novel ultrafast multipass laser amplifier design optimized for sub-millijoule output energy and capable of being operated at repetition rates exceeding 40 kHz. This ti:sapphire based system makes use of a grism based stretcher, a cryogenically cooled ti:sapphire crystal and an astigmatically compensated multipass amplifier design that allows for pumping with significantly lower pump pulse energies than has been demonstrated to date. We also make use of the downchirped pulse amplification scheme to minimize loss in the pulse compression process. Preliminary experiments demonstrate an output pulse energy of 290 muJ at 10 kHz and 270 muJ at 15 kHz with a pulse duration of 36 fs.
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17
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Zimmermann J, Oakman EL, Thorpe IF, Shi X, Abbyad P, Brooks CL, Boxer SG, Romesberg FE. Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc Natl Acad Sci U S A 2006; 103:13722-7. [PMID: 16954202 PMCID: PMC1564241 DOI: 10.1073/pnas.0603282103] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolution of proteins with novel function is thought to start from precursor proteins that are conformationally heterogeneous. The corresponding genes may be duplicated and then mutated to select and optimize a specific conformation. However, testing this idea has been difficult because of the challenge of quantifying protein flexibility and conformational heterogeneity as a function of evolution. Here, we report the characterization of protein heterogeneity and dynamics as a function of evolution for the antifluorescein antibody 4-4-20. Using nonlinear laser spectroscopy, surface plasmon resonance, and molecular dynamics simulations, we demonstrate that evolution localized the Ab-combining site from a heterogeneous ensemble of conformations to a single conformation by introducing mutations that act cooperatively and over significant distances to rigidify the protein. This study demonstrates how protein dynamics may be tailored by evolution and has important implications for our understanding of how novel protein functions are evolved.
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Affiliation(s)
| | | | - Ian F. Thorpe
- Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037; and
| | - Xinghua Shi
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Paul Abbyad
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Charles L. Brooks
- Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037; and
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Floyd E. Romesberg
- Departments of *Chemistry and
- To whom correspondence should be addressed. E-mail:
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18
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Cho BM, Carlsson CF, Jimenez R. Photon echo spectroscopy of porphyrins and heme proteins: Effects of quasidegenerate electronic structure on the peak shift decay. J Chem Phys 2006; 124:144905. [PMID: 16626243 DOI: 10.1063/1.2186318] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Three pulse photon echo peak shift spectroscopy and transient grating measurements on Zn-substituted cytochrome c, Zn-tetraphenylporphyrin, and Zn-protoporphyrin IX are reported. The effects of protein conformation, axial ligation, and solvent are investigated. Numerical simulations of the peak shift and transient grating experiments are presented. The simulations employed recently derived optical response functions for square-symmetric molecules with doubly degenerate excited states. Simulations exploring the effects of excited-state energy splitting, symmetric and asymmetric fluctuations, and excited-state lifetime show that the time scales of the peak shift decay in the three-level system largely reflect the same dynamics as in the two-level system. However, the asymptotic peak shift, which is a clear indicator of inhomogeneous broadening in a two-level system, must be interpreted more carefully for three-level systems, as it is also influenced by the magnitude of the excited-state splitting. The calculated signals qualitatively reproduce the data.
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Affiliation(s)
- Byung Moon Cho
- JILA, University of Colorado and National Institute of Standards and Technology, Boulder, Colorado 80309-0440, USA
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19
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Excited state dynamics of a conformationally disordered conjugated polymer: A comparison of solutions and film. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2005.04.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mohammed OF, Dreyer J, Magnes BZ, Pines E, Nibbering ETJ. Solvent-Dependent Photoacidity State of Pyranine Monitored by Transient Mid-Infrared Spectroscopy. Chemphyschem 2005; 6:625-36. [PMID: 15881578 DOI: 10.1002/cphc.200400510] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We investigate with femtosecond mid-infrared spectroscopy the vibrational-mode characteristics of the electronic states involved in the excited-state dynamics of pyranine (HPTS) that ultimately lead to efficient proton (deuteron) transfer in H2O (D2O). We also study the methoxy derivative of pyranine (MPTS), which is similar in electronic structure but does not have the photoacidity property. We compare the observed vibrational band patterns of MPTS and HPTS after electronic excitation in the solvents: deuterated dimethylsulfoxide, deuterated methanol and H2O/D2O, from which we conclude that for MPTS and HPTS photoacids the first excited singlet state appears to have charge-transfer (CT) properties in water within our time resolution (150 fs), whereas in aprotic dimethylsulfoxide the photoacid appears to be in a non-polar electronic excited state, and in methanol (less polar and less acidic than water) the behaviour is intermediate between these two extremes. For the fingerprint vibrations we do not observe dynamics on a time scale of a few picoseconds, and with our results obtained on the O-H stretching vibration we argue that the dynamic behaviour observed in previous UV/Vis pump-probe studies is likely to be related to solvation dynamics.
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Affiliation(s)
- Omar F Mohammed
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, 12489 Berlin (Germany)
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21
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Cho BM, Walker RC, Amer H, Mercer I, Klug DR, Gould IR. Effect of Adiabaticity on Electron Dynamics in Zinc Myoglobin. J Phys Chem B 2005; 109:5954-61. [PMID: 16851650 DOI: 10.1021/jp0470748] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Electron-vibration coupling in zinc substituted myoglobin has been calculated using a quantum mechanical/molecular mechanical method. The methodology has been tested by a direct comparison of the calculated optical observables, the steady-state optical spectra and three-pulse-photon-echo-peak-shift (3PEPS) function, to those experimentally measured showing a qualitative agreement. A range of experiments and calculations were performed to explain the discrepancies, which lead to the conclusion that the discrepancy originates from adiabatic coupling of the two nearly degenerate electronic transitions.
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Affiliation(s)
- Byung Moon Cho
- Biological and Biophysical Chemistry Group and Molecular Dynamics Group, Department of Chemistry, Imperial College London, London, U.K
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Varnavski O, Goodson T, Sukhomlinova L, Twieg R. Ultrafast Exciton Dynamics in a Branched Molecule Investigated by Time-Resolved Fluorescence, Transient Absorption, and Three-Pulse Photon Echo Peak Shift Measurements. J Phys Chem B 2004. [DOI: 10.1021/jp0495996] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Jimenez R, Salazar G, Yin J, Joo T, Romesberg FE. Protein dynamics and the immunological evolution of molecular recognition. Proc Natl Acad Sci U S A 2004; 101:3803-8. [PMID: 15001706 PMCID: PMC374325 DOI: 10.1073/pnas.0305745101] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While it is accepted that protein flexibility plays a role in protein folding, catalysis, and molecular recognition, few techniques are capable of the rigorous measurement of protein motions required to quantify flexibility. Three-pulse photon echo shift spectroscopy can be used to measure the time scale of protein motions, and we have used this technique, along with steady-state spectroscopy and binding and structural data, to examine the immunological evolution of protein flexibility in an anti-fluorescein antibody. Two light chain somatic mutations increase affinity for fluorescein by 12-fold but also significantly affect flexibility. Specifically, a rigidification of the protein is seen in each of three observable motions; two slower motions undergo decreased amplitudes of displacement, by 3- and 20-fold, respectively, in response to an applied force, and the distribution associated with the amplitude of a faster motion is narrowed upon somatic mutation. The somatic mutations appear to rigidify the antibody-fluorescein complex by more strongly anchoring fluorescein to the protein and by more tightly packing the complex. The data demonstrate that in addition to affinity, antibody dynamics are systematically manipulated during affinity maturation, and they imply that the evolution of protein flexibility may be a central component of the immune response. The results also reflect the type of protein rigidification that may be important for other biological interactions, such as protein-protein, protein-ligand or protein-drug, and enzyme-substrate recognition.
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Affiliation(s)
- Ralph Jimenez
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, Maildrop CVN22, La Jolla, CA 92037, USA
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Giraud G, Karolin J, Wynne K. Low-frequency modes of peptides and globular proteins in solution observed by ultrafast OHD-RIKES spectroscopy. Biophys J 2003; 85:1903-13. [PMID: 12944303 PMCID: PMC1303362 DOI: 10.1016/s0006-3495(03)74618-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The low-frequency (1-200 cm(-1)) vibrational spectra of peptides and proteins in solution have been investigated with ultrafast optical heterodyne-detected Raman-induced Kerr-effect spectroscopy (OHD-RIKES). Spectra have been obtained for di-L-alanine (ALA(2)) and the alpha-helical peptide poly-L-alanine (PLA) in dichloroacetic acid solution. The poly-L-alanine spectrum shows extra amplitude compared to the di-L-alanine spectrum, which can be explained by the secondary structure of the former. The globular proteins lysozyme, alpha-lactalbumin, pepsin, and beta-lactoglobulin in aqueous solution have been studied to determine the possible influence of secondary or tertiary structure on the low-frequency spectra. The spectra of the globular proteins have been analyzed in terms of three nondiffusive Brownian oscillators. The lowest frequency oscillator corresponds to the so-called Boson peak observed in inelastic neutron scattering (INS). The remaining two oscillators are not observed in inelastic neutron scattering, do therefore not involve significant motion of hydrogen atoms, and may be associated with delocalized backbone torsions.
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Affiliation(s)
- Gerard Giraud
- Department of Physics, University of Strathclyde, Glasgow G4 0NG, Scotland, United Kingdom
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25
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Romesberg FE. Multidisciplinary experimental approaches to characterizing biomolecular dynamics. Chembiochem 2003; 4:563-71. [PMID: 12851924 DOI: 10.1002/cbic.200300572] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, Maildrop CVN22, La Jolla, CA 92037, USA.
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26
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Eaves JD, Fecko CJ, Stevens AL, Peng P, Tokmakoff A. Polarization-selective femtosecond Raman spectroscopy of low-frequency motions in hydrated protein films. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)00890-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Nagasawa Y, Seike K, Muromoto T, Okada T. Two-Dimensional Analysis of Integrated Three-Pulse Photon Echo Signals of Nile Blue Doped in PMMA. J Phys Chem A 2003. [DOI: 10.1021/jp027012m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yutaka Nagasawa
- Department of Chemistry, Graduate School of Engineering Science, and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kazushige Seike
- Department of Chemistry, Graduate School of Engineering Science, and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Takayuki Muromoto
- Department of Chemistry, Graduate School of Engineering Science, and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tadashi Okada
- Department of Chemistry, Graduate School of Engineering Science, and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Nagasawa Y, Watanabe A, Takikawa H, Okada T. Solute Dependence of Three Pulse Photon Echo Peak Shift Measurements in Methanol Solution. J Phys Chem A 2003. [DOI: 10.1021/jp0271559] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yutaka Nagasawa
- Department of Chemistry, Graduate School of Engineering Science and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ayako Watanabe
- Department of Chemistry, Graduate School of Engineering Science and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Hiroko Takikawa
- Department of Chemistry, Graduate School of Engineering Science and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tadashi Okada
- Department of Chemistry, Graduate School of Engineering Science and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Jimenez R, Salazar G, Baldridge KK, Romesberg FE. Flexibility and molecular recognition in the immune system. Proc Natl Acad Sci U S A 2003; 100:92-7. [PMID: 12518056 PMCID: PMC140891 DOI: 10.1073/pnas.262411399] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photon echo spectroscopy has been used to measure the response of three antibody-binding sites to perturbation from electronic excitation of a bound antigen, fluorescein. The three antibodies show motions that range in time scale from tens of femtoseconds to nanoseconds. Relative to the others, one antibody, 4-4-20, possesses a rigid binding site that likely results from a short and inflexible heavy chain complementarity-determining region 3 (HCDR3) loop and a critical Tyr that acts as a "molecular splint," rigidifying the antigen across its most flexible internal degree of freedom. The remaining two antibodies, 34F10 and 40G4, despite being generated against the same antigen, possess binding sites that are considerably more flexible. The more flexible combining sites likely result from longer HCDR3 loops and a deletion in the light chain complementarity-determining region 1 (LCDR1) that removes the critical Tyr residue. The binding site flexibilities may result in varying mechanisms of antigen recognition including lock-and-key, induced-fit, and conformational selection.
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Affiliation(s)
- Ralph Jimenez
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, Mail Drop CVN22, La Jolla, CA 92037, USA
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