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Portillo-Ledesma S, Schlick T. Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019; 10. [PMID: 34046090 DOI: 10.1002/wcms.1434] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromatin structure, dynamics, and function are being intensely investigated by a variety of methods, including microscopy, X-ray diffraction, nuclear magnetic resonance, biochemical crosslinking, chromosome conformation capture, and computation. A range of experimental techniques combined with modeling is clearly valuable to help interpret experimental data and, importantly, generate configurations and mechanisms related to the 3D organization and function of the genome. Contact maps, in particular, as obtained by a variety of chromosome conformation capture methods, are of increasing interest due to their implications on genome structure and regulation on many levels. In this perspective, using seven examples from our group's studies, we illustrate how molecular modeling can help interpret such experimental data. Specifically, we show how computed contact maps related to experimental systems can be used to explain structures of nucleosomes, chromatin higher-order folding, domain segregation mechanisms, gene organization, and the effect on chromatin structure of external and internal fiber parameters, such as nucleosome positioning, presence of nucleosome free regions, histone posttranslational modifications, and linker histone binding. We argue that such computations on multiple spatial and temporal scales will be increasingly important for the integration of genomic, epigenomic, and biophysical data on chromatin structure and related cellular processes.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, New York, 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, New York, 10003, USA.,Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, New York, 10012, USA.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200062, China
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Zhang X, Bao L, Wu YY, Zhu XL, Tan ZJ. Radial distribution function of semiflexible oligomers with stretching flexibility. J Chem Phys 2018; 147:054901. [PMID: 28789545 DOI: 10.1063/1.4991689] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The radial distribution of the end-to-end distance Ree is crucial for quantifying the global size and flexibility of a linear polymer. For semiflexible polymers, several analytical formulas have been derived for the radial distribution of Ree ignoring the stretching flexibility. However, for semiflexible oligomers, such as DNA or RNA, the stretching flexibility can be rather pronounced and can significantly affect the radial distribution of Ree. In this study, we obtained an extended formula that includes the stretch modulus to describe the distribution of Ree for semiflexible oligomers on the basis of previous formulas for semiflexible polymers without stretching flexibility. The extended formula was validated by extensive Monte Carlo simulations over wide ranges of the stretch modulus and persistence length, as well as all-atom molecular dynamics simulations of short DNAs and RNAs. Additionally, our analyses showed that the effect of stretching flexibility on the distribution of Ree becomes negligible for DNAs longer than ∼130 base pairs and RNAs longer than ∼240 base pairs.
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Affiliation(s)
- Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Lei Bao
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yuan-Yan Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xiao-Long Zhu
- Department of Physics, School of Physics and Information Engineering, Jianghan University, Wuhan 430056, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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3
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Nizovtseva EV, Clauvelin N, Todolli S, Polikanov YS, Kulaeva OI, Wengrzynek S, Olson WK, Studitsky VM. Nucleosome-free DNA regions differentially affect distant communication in chromatin. Nucleic Acids Res 2017; 45:3059-3067. [PMID: 27940560 PMCID: PMC5389534 DOI: 10.1093/nar/gkw1240] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/29/2016] [Indexed: 11/13/2022] Open
Abstract
Communication between distantly spaced genomic regions is one of the key features of gene regulation in eukaryotes. Chromatin per se can stimulate efficient enhancer-promoter communication (EPC); however, the role of chromatin structure and dynamics in this process remains poorly understood. Here we show that nucleosome spacing and the presence of nucleosome-free DNA regions can modulate chromatin structure/dynamics and, in turn, affect the rate of EPC in vitro and in silico. Increasing the length of internucleosomal linker DNA from 25 to 60 bp results in more efficient EPC. The presence of longer nucleosome-free DNA regions can positively or negatively affect the rate of EPC, depending upon the length and location of the DNA region within the chromatin fiber. Thus the presence of histone-free DNA regions can differentially affect the efficiency of EPC, suggesting that gene regulation over a distance could be modulated by changes in the length of internucleosomal DNA spacers.
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Affiliation(s)
- Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Nicolas Clauvelin
- Department of Chemistry and Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Stefjord Todolli
- Department of Chemistry and Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Yury S Polikanov
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Olga I Kulaeva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA.,Biology Faculty, Moscow State University, Moscow 119991, Russia
| | - Scott Wengrzynek
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Wilma K Olson
- Department of Chemistry and Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Laboratory of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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Nizovtseva EV, Todolli S, Olson WK, Studitsky VM. Towards quantitative analysis of gene regulation by enhancers. Epigenomics 2017; 9:1219-1231. [PMID: 28799793 DOI: 10.2217/epi-2017-0061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Enhancers are regulatory DNA sequences that can activate transcription over large distances. Recent studies have revealed the widespread role of distant activation in eukaryotic gene regulation and in the development of various human diseases, including cancer. Here we review recent progress in the field, focusing on new experimental and computational approaches that quantify the role of chromatin structure and dynamics during enhancer-promoter interactions in vitro and in vivo.
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Affiliation(s)
- Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Stefjord Todolli
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Wilma K Olson
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Biology Faculty, Moscow State University, Moscow 119991, Russia.,Laboratory of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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Bascom G, Schlick T. Linking Chromatin Fibers to Gene Folding by Hierarchical Looping. Biophys J 2017; 112:434-445. [PMID: 28153411 DOI: 10.1016/j.bpj.2017.01.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/16/2022] Open
Abstract
While much is known about DNA structure on the basepair level, this scale represents only a fraction of the structural levels involved in folding the genomic material. With recent advances in experimental and theoretical techniques, a variety of structures have been observed on the fiber, gene, and chromosome levels of genome organization. Here we view chromatin architecture from nucleosomes and fibers to genes and chromosomes, highlighting the rich structural diversity and fiber fluidity emerging from both experimental and theoretical techniques. In this context, we discuss our recently proposed folding mechanism, which we call "hierarchical looping", similar to rope flaking used in mountain climbing, where 10-nm zigzag chromatin fibers are compacted laterally into self-associating loops which then stack and fold in space. We propose that hierarchical looping may act as a bridge between fibers and genes as well as provide a mechanism to relate key features of interphase and metaphase chromosome architecture to genome structural changes. This motif emerged by analysis of ultrastructural internucleosome contact data by electron microscopy-assisted nucleosome interaction capture cross-linking experiments, in combination with mesoscale modeling. We suggest that while the local folding of chromatin can be regulated at the fiber level by adjustment of internal factors such as linker-histone binding affinities, linker DNA lengths, and divalent ion levels, hierarchical looping on the gene level can additionally be controlled by posttranslational modifications and external factors such as polycomb group proteins. From a combination of 3C data and mesoscale modeling, we suggest that hierarchical looping could also play a role in epigenetic gene silencing, as stacked loops may occlude access to transcription start sites. With advances in crystallography, single-molecule in vitro biochemistry, in vivo imaging techniques, and genome-wide contact data experiments, various modeling approaches are allowing for previously unavailable structural interpretation of these data at multiple spatial and temporal scales. An unprecedented level of productivity and opportunity is on the horizon for the chromatin structure field.
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Affiliation(s)
- Gavin Bascom
- Department of Chemistry, New York University, New York, New York
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York; Courant Institute of Mathematical Sciences, New York University, New York, New York; New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai, China.
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Todolli S, Perez PJ, Clauvelin N, Olson WK. Contributions of Sequence to the Higher-Order Structures of DNA. Biophys J 2016; 112:416-426. [PMID: 27955889 DOI: 10.1016/j.bpj.2016.11.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/11/2016] [Accepted: 11/15/2016] [Indexed: 11/17/2022] Open
Abstract
One of the critical unanswered questions in genome biophysics is how the primary sequence of DNA bases influences the global properties of very-long-chain molecules. The local sequence-dependent features of DNA found in high-resolution structures introduce irregularities in the disposition of adjacent residues that facilitate the specific binding of proteins and modulate the global folding and interactions of double helices with hundreds of basepairs. These features also determine the positions of nucleosomes on DNA and the lengths of the interspersed DNA linkers. Like the patterns of basepair association within DNA, the arrangements of nucleosomes in chromatin modulate the properties of longer polymers. The intrachromosomal loops detected in genomic studies contain hundreds of nucleosomes, and given that the simulated configurations of chromatin depend on the lengths of linker DNA, the formation of these loops may reflect sequence-dependent information encoded within the positioning of the nucleosomes. With knowledge of the positions of nucleosomes on a given genome, methods are now at hand to estimate the looping propensities of chromatin in terms of the spacing of nucleosomes and to make a direct connection between the DNA base sequence and larger-scale chromatin folding.
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Affiliation(s)
- Stefjord Todolli
- Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Pamela J Perez
- Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Nicolas Clauvelin
- Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Wilma K Olson
- Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, New Jersey; Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey.
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7
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Iacomino G, Picariello G, Sbrana F, Raiteri R, D'Agostino L. DNA-HMGB1 interaction: The nuclear aggregates of polyamine mediation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1402-10. [PMID: 27451951 DOI: 10.1016/j.bbapap.2016.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/13/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022]
Abstract
Nuclear aggregates of polyamines (NAPs) are supramolecular compounds generated by the self-assembly of protonated nuclear polyamines (spermine, spermidine and putrescine) and phosphate ions. In the presence of genomic DNA, the hierarchical process of self-structuring ultimately produces nanotube-like polymers that envelop the double helix. Because of their modular nature and their aggregation-disaggregation dynamics, NAPs confer plasticity and flexibility to DNA. Through the disposition of charges, NAPs also enable a bidirectional stream of information between the genome and interacting moieties. High mobility group (HMG) B1 is a non-histone chromosomal protein that binds to DNA and that influences multiple nuclear processes. Because genomic DNA binds to either NAPs or HMGB1 protein, we explored the ability of in vitro self-assembled NAPs (ivNAPs) to mediate the DNA-HMGB1 interaction. To this end, we structured DNA-NAPs-HMGB1 and DNA-HMGB1-NAPs ternary complexes in vitro through opportune sequential incubations. Mobility shift electrophoresis and atomic force microscopy showed that the DNA-ivNAPs-HGMB1 complex had conformational assets supposedly more suitable those of the DNA-HGMB1-ivNAPs to comply with the physiological and functional requirements of DNA. Our findings indicated that ivNAPs act as mediators of the DNA-HMGB1 interaction.
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Affiliation(s)
- Giuseppe Iacomino
- Istituto di Scienze dell'Alimentazione - CNR, Via Roma 64 - 83100, Avellino, Italy
| | - Gianluca Picariello
- Istituto di Scienze dell'Alimentazione - CNR, Via Roma 64 - 83100, Avellino, Italy
| | - Francesca Sbrana
- Istituto di Biofisica - CNR, Via De Marini 6 - 16149, Genova, Italy
| | - Roberto Raiteri
- Istituto di Biofisica - CNR, Via De Marini 6 - 16149, Genova, Italy; Dipartimento di Informatica, Bioingegneria, Robotica ed Ingegneria dei Sistemi - Università degli Studi di Genova, Via All'Opera Pia 13 - 16145, Genova, Italy
| | - Luciano D'Agostino
- Istituto di Scienze dell'Alimentazione - CNR, Via Roma 64 - 83100, Avellino, Italy.
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8
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Biophysical Reviews publications on DNA structure and function that complement this Special Issue on DNA supercoiling. Biophys Rev 2016; 8:157-158. [PMID: 28510214 DOI: 10.1007/s12551-016-0213-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022] Open
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9
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Wu YY, Bao L, Zhang X, Tan ZJ. Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs. J Chem Phys 2016; 142:125103. [PMID: 25833610 DOI: 10.1063/1.4915539] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5-50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ∼6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ∼29 nm to ∼45 nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ∼6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with lp ∼ 50 nm.
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Affiliation(s)
- Yuan-Yan Wu
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Lei Bao
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xi Zhang
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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Yusufaly TI, Li Y, Singh G, Olson WK. Arginine-phosphate salt bridges between histones and DNA: intermolecular actuators that control nucleosome architecture. J Chem Phys 2015; 141:165102. [PMID: 25362343 DOI: 10.1063/1.4897978] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. Principal component analysis reveals that the configurational fluctuations of the sugar-phosphate backbone display sequence-specific directionality and variability, and clustering of nucleosome crystal structures identifies two major salt-bridge configurations: a monodentate form in which the arginine end-group guanidinium only forms one hydrogen bond with the phosphate, and a bidentate form in which it forms two. Density functional theory calculations highlight that the combination of sequence, denticity, and salt-bridge positioning enables the histones to apply a tunable mechanochemical stress to the DNA via precise and specific activation of backbone deformations. The results suggest that selection for specific placements of van der Waals contacts, with high-precision control of the spatial distribution of intermolecular forces, may serve as an underlying evolutionary design principle for the structure and function of nucleosomes, a conjecture that is corroborated by previous experimental studies.
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Affiliation(s)
- Tahir I Yusufaly
- Department of Physics and Astronomy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Yun Li
- Department of Chemistry and Biochemistry, Delaware Valley College, Doylestown, Pennsylvania 18901, USA
| | - Gautam Singh
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Wilma K Olson
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
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Clauvelin N, Lo P, Kulaeva OI, Nizovtseva EV, Diaz-Montes J, Zola J, Parashar M, Studitsky VM, Olson WK. Nucleosome positioning and composition modulate in silico chromatin flexibility. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064112. [PMID: 25564155 PMCID: PMC4492108 DOI: 10.1088/0953-8984/27/6/064112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes-the familiar assemblies of ∼150 DNA base pairs and eight histone proteins-found on chromatin fibers. Here we introduce a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs. We explore the effects of nucleosome positioning and the presence or absence of cationic N-terminal histone tails on the 'local' inter-nucleosomal interactions and the global deformations of the simulated chains. The correspondence between the predicted and observed effects of nucleosome composition and numbers on the long-range communication between the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We also extract effective nucleosome-nucleosome potentials from the simulations and implement the potentials in a larger-scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable effect of nucleosome spacing on chromatin flexibility, with small changes in DNA linker length significantly altering the interactions of nucleosomes and the dimensions of the fiber as a whole. In addition, we find that these changes in nucleosome positioning influence the statistical properties of long chromatin constructs. That is, simulated chromatin fibers with the same number of nucleosomes exhibit polymeric behaviors ranging from Gaussian to worm-like, depending upon nucleosome spacing. These findings suggest that the physical and mechanical properties of chromatin can span a wide range of behaviors, depending on nucleosome positioning, and that care must be taken in the choice of models used to interpret the experimental properties of long chromatin fibers.
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Affiliation(s)
- N Clauvelin
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers the State University of New Jersey, Piscataway, NJ 08854, USA
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