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Submissions from 2020

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HEM1 deficiency disrupts mTORC2 and F-actin control in inherited immunodysregulatory disease, Sarah A. Cook, William A. Comrie, Morgan Similuk, Andrew J. Oler, Aiman J. Faruqi, Sheng Yang, D. Eric Anderson, Susan Price, Margery Smelkinson, Baoyu Chen, V. Koneti Rao, Michael J. Lenardo, and et al.

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TOR mediates the autophagy response to altered nucleotide homeostasis in a ribonuclease mutant, Zakayo Kazibwe, Junmarie Soto-Burgos, Gustavo C. Macintosh, and Diane C. Bassham

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Probing enzymatic structure-function in the di-hydroxylating sesquiterpene synthase ZmEDS, Jin Liang, Liping Wang, Jiang Liu, Qinqin Shen, Jingye Fu, Reuben J. Peters, and Qiang Wang

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The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration, Xiangdong Pu, Zhen Li, Ya Tian, Ranran Gao, Lijun Hao, Yating Hu, Chunnian He, Wei Sun, Meimei Xu, Reuben J. Peters, Yves Van de Peer, Zhichao Xu, and Jingyuan Song

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Site-specific N-glycan Analysis of Antibody-binding Fc γ Receptors from Primary Human Monocytes, Jacob T. Roberts, Kashyap R. Patel, and Adam W. Barb

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Genome of Tripterygium wilfordii and identification of cytochrome P450 involved in triptolide biosynthesis, Lichan Tu, Ping Su, Zhongren Zhang, Linhui Gao, Jiadian Wang, Tianyuan Hu, Jiawei Zhou, Yifeng Zhang, Yujun Zhao, Yuan Liu, Yadi Song, Yuru Tong, Yun Lu, Jian Yang, Cao Xu, Meirong Jia, Reuben J. Peters, Luqi Huang, and Wei Gao

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Why are momilactones always associated with biosynthetic gene clusters in plants?, Juan Zhang and Reuben J. Peters

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Introducing selective agrochemical manipulation of gibberellin metabolism into a cereal crop, Juan Zhang, Yushi Zhang, Jiapeng Xing, Haiyue Yu, Rui Zhang, Yiyao Chen, Delin Zhang, Ping Yin, Xiaoli Tian, Qiang Wang, Liusheng Duan, Mingcai Zhang, Reuben J. Peters, and Zhaohu Li

Submissions from 2019

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Induction of ethylene inhibits development of soybean sudden death syndrome by inducing defense-related genes and reducing Fusarium virguliforme growth, Noor A. Abdelsamad, Gustavo C. Macintosh, and Leonor F.S. Leandro

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A single-cell platform for reconstituting and characterizing fatty acid elongase component enzymes, Alexis A. Campbell, Kenna E. Stenback, Kayla Flyckt, Trang Hoang, M. Ann Perera, and Basil J. Nikolau

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Entropy, Fluctuations, and Disordered Proteins, Eshel Faraggi, A. Keith Dunker, Robert L. Jernigan, and Andrzej Kloczkowski

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CYP72A enzymes catalyse 13-hydrolyzation of gibberellins, Juan He, Qingwen Chen, Peiyong Xin, Jia Yuan, Yihua Ma, Xuemei Wang, Meimei Xu, Jinfang Chu, Reuben J. Peters, and Guodong Wang

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Identification of RoCYP01 (CYP716A155) enables construction of engineered yeast for high-yield production of betulinic acid, Jiajian Huang, Wenlong Zha, Tianyue An, Hua Dong, Ying Huang, Dong Wang, Rongmin Yu, Lixin Duan, Xueli Zhang, Reuben J. Peters, Zhubo Dai, and Jiachen Zi

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Aptamers for Diagnostics with Applications for Infectious Diseases, Muslum Ilgu, Rezzan Fazlioglu, Meric Ozturk, Yasemin Ozsurekci, and Marit Nilsen-Hamilton

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Combinatorial biosynthesis and the basis for substrate promiscuity in class I diterpene synthases, Meirong Jia, Sambit K. Mishra, Samuel Tufts, Robert L. Jernigan, and Reuben J. Peters

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Switching on a Nontraditional Enzymatic Base—Deprotonation by Serine in the ent-Kaurene Synthase from Bradyrhizobium japonicum, Meirong Jia, Yue Zhang, Justin B. Siegel, Dean J. Tantillo, and Reuben J. Peters

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The Ins and Outs of Autophagic Ribosome Turnover, Zakayo Kazibwe, Ang-Yu Liu, Gustavo C. Macintosh, and Diane C. Bassham

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Characterizing and Predicting Protein Hinges for Mechanistic Insight, Pranav M. Khade, Ambuj Kumar, and Robert L. Jernigan

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Conserved bases for the initial cyclase in gibberellin biosynthesis: from bacteria to plants, Cody Lemke, Kevin C. Potter, Samuel Schulte, and Reuben J. Peters

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Gene pyramids and the balancing act of keeping pests at bay, Gustavo C. Macintosh

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Coupling Dynamics and Evolutionary Information with Structure to Identify Protein Regulatory and Functional Binding Sites, Sambit Kumar Mishra, Gaurav Kandoi, and Robert L. Jernigan

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Isoprenyl diphosphate synthases: the chain length determining step in terpene biosynthesis, Raimund Nagel, Axel Schmidt, and Reuben J. Peters

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Primary Human Natural Killer Cells Retain Proinflammatory IgG1 at the Cell Surface and Express CD16a Glycoforms with Donor-dependent Variability, Kashyap R. Patel, Joel D. Nott, and Adam W. Barb

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Multiple Variables at the Leukocyte Cell Surface Impact Fc γ Receptor-Dependent Mechanisms, Kashyap R. Patel, Jacob T. Roberts, and Adam W. Barb

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The genome of the medicinal plant Andrographis paniculata provides insight into the biosynthesis of the bioactive diterpenoid neoandrographolide, Wei Sun, Liang Leng, Qinggang Yin, Meimei Xu, Mingkun Huang, Zhichao Xu, Yujun Zhang, Hui Yao, Caixia Wang, Chao Xiong, Sha Chen, Chunhong Jiang, Ning Xie, Xilong Zheng, Chi Song, Reuben J. Peters, and Shilin Chen

Submissions from 2018

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Mouse IgG2c Fc loop residues promote greater receptor-binding affinity than mouse IgG2b or human IgG1, Daniel J. Falconer and Adam W. Barb

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SeqStruct : A New Amino Acid Similarity Matrix Based on Sequence Correlations and Structural Contacts Yields Sequence-Structure Congruence, Kejue Jia and Robert L. Jernigan

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Changing Face: A Key Residue for the Addition of Water by Sclareol Synthase, Meirong Jia, Terrence E. O'Brien, Yue Zhang, Justin B. Siegel, Dean J. Tantillo, and Reuben J. Peters

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Direct production of dihydroxylated sesquiterpenoids by a maize terpene synthase, Jin Liang, Jiang Liu, Reid Brown, Meirong Jia, Ke Zhou, Reuben J. Peters, and Qiang Wang

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Aptamer-enabled uptake of small molecule ligands, Supipi Liyamali Auwardt, Yeon-Jung Seo, Muslum Ilgu, Judhajeet Ray, Robert R. Feldges, Shambhavi Shubham, Lee Bendickson, Howard A. Levine, and Marit Nilsen-Hamilton

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Inferring Roles in Defense from Metabolic Allocation of Rice Diterpenoids, Xuan Lu, Juan Zhang, Benjamin Brown, Riqing Li, Julio Rodríguez-Romero, Aileen Berasategui, Bo Liu, Meimei Xu, Dangping Luo, Zhiqiang Pan, Scott R. Baerson, Jonathan Gershenzon, Zhaohu Li, Ane Sesma, Bing Yang, and Reuben J. Peters

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Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics, Sambit Kumar Mishra and Robert L. Jernigan

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A Third Class: Functional Gibberellin Biosynthetic Operon in Beta-Proteobacteria, Raimund Nagel, John E. Bieber, Mark G. Schmidt-Dannert, Ryan S. Nett, and Reuben J. Peters

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Diverging Mechanisms: Cytochrome‐P450‐Catalyzed Demethylation and γ‐Lactone Formation in Bacterial Gibberellin Biosynthesis, Raimund Nagel and Reuben J. Peters

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Probing the specificity of CYP112 in bacterial gibberellin biosynthesis, Raimund Nagel and Reuben J. Peters

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Arginine in the FARM and SARM: A Role in Chain-Length Determination for Arginine in the Aspartate-Rich Motifs of Isoprenyl Diphosphate Synthases from Mycobacterium tuberculosis, Raimund Nagel, Jill A. Thomas, Faith A. Adekunle, Francis M. Mann, and Reuben J. Peters

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Restricted processing of CD16a/Fc γ receptor IIIa N-glycans from primary human NK cells impacts structure and function, Kashyap R. Patel, Jacob T. Roberts, Ganesh P. Subedi, and Adam W. Barb

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Continuous Interdomain Orientation Distributions Reveal Components of Binding Thermodynamics, Yang Qi, Jeffrey W. Martin, Adam W. Barb, Francois Thelot, Anthony Yan, Bruce R. Donald, and Terrence G. Oas

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A single amino acid distorts the Fc γ receptor IIIb/CD16b structure upon binding immunoglobulin G1 and reduces affinity relative to CD16a, Jacob T. Roberts and Adam W. Barb

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Comparisons of Protein Dynamics from Experimental Structure Ensembles, Molecular Dynamics Ensembles, and Coarse-Grained Elastic Network Models, Kannan Sankar, Sambit K. Mishra, and Robert L. Jernigan

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Catalytic Bases and Stereocontrol in Lamiaceae Class II Diterpene Cyclases, Samuel Schulte, Kevin C. Potter, Cody Lemke, and Reuben J. Peters

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A 2′FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein, Shambhavi Shubham, Jan Hoinka, Soma Banerjee, Emma Swanson, Jacob A. Dillard, Nicholas J. Lennemann, Teresa M. Przytycka, Wendy Maury, and Marit Nilsen-Hamilton

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CD16a with oligomannose-type N-glycans is the only “low-affinity” Fc γ receptor that binds the IgG crystallizable fragment with high affinity in vitro, Ganesh P. Subedi and Adam W. Barb

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Identification and functional characterization of diterpene synthases for triptolide biosynthesis from Tripterygium wilfordii, Ping Su, Hongyu Guan, Yujun Zhao, Yuru Tong, Meimei Xu, Yifeng Zhang, Tianyuan Hu, Jian Yang, Qiqing Cheng, Linhui Gao, Yujia Liu, Jiawei Zhou, Reuben J. Peters, Luqi Huang, and Wei Gao

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Direct Determination of the Site of Addition of Glucosyl Units to Maltooligosaccharide Acceptors Catalyzed by Maize Starch Synthase I, Ying Xie, Adam W. Barb, Tracie A. Hennen-Bierwagen, and Alan M. Myers

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Premutilin Synthase: Ring Rearrangement by a Class II Diterpene Cyclase, Meimei Xu, Meirong Jia, Young J. Hong, Xihou Yin, Dean J. Tantillo, Philip J. Proteau, and Reuben J. Peters

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Evidence for a role of spindle matrix formation in cell cycle progression by antibody perturbation, Changfu Yao, Chao Wang, Yeran Li, Michael Zavortink, Vincent Archambault, Jack Girton, Kristen M. Johansen, and Jorgen Johansen

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A Dendritic Guidance Receptor Complex Brings Together Distinct Actin Regulators to Drive Efficient F-Actin Assembly and Branching, Wei Zhou, Xintong Dong, Timothy R. Broederdorf, Ao Shen, Daniel A. Kramer, Rebecca Shi, Xing Liang, David M. Miller III, Yang K. Xiang, Ryohei Yasuda, Baoyu Chen, and Kang Shen

Submissions from 2017

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Rac1 GTPase activates the WAVE regulatory complex through two distinct binding sites, Baoyu Chen, Hui-Ting Chou, Chad A. Brautigam, Wenmin Xing, Sheng Yang, Lisa Henry, Lynda K. Doolittle, Thomas Walz, and Michael K. Rosen

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Biosynthesis of Diterpenoids in Tripterygium Adventitious Root Cultures, Fainmarinat S. Inabuy, Justin T. Fischedick, Iris Lange, Michael Hartmann, Narayanan Srividya, Amber N. Parrish, Meimei Xu, Reuben J. Peters, and B. Markus Lange

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cis or trans with class II diterpene cyclases, Meirong Jia and Reuben J. Peters

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A Pair of Residues That Interactively Affect Diterpene Synthase Product Outcome, Meirong Jia, Samuel Tufts, Samuel Schulte, and Reuben J. Peters

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H2Av facilitates H3S10 phosphorylation but is not required for heat shock-induced chromatin decondensation or transcriptional elongation, Yeran Li, Chao Wang, Weili Cai, Saheli Sengupta, Michael Zavortink, Huai Deng, Jack Girton, Jorgen Johansen, and Kristen M. Johansen

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18O2 labeling experiments illuminate the oxidation of ent-kaurene in bacterial gibberellin biosynthesis, Raimund Nagel and Reuben J. Peters

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Investigating the Phylogenetic Range of Gibberellin Biosynthesis in Bacteria, Raimund Nagel and Reuben J. Peters

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An operon for production of bioactive gibberellin A4 phytohormone with wide distribution in the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola, Raimund Nagel, Paula C. G. Turrini, Ryan S. Nett, Jan E. Leach, Valérie Verdier, Marie-Anne Van Sluys, and Reuben J. Peters

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Characterization of CYP115 As a Gibberellin 3-Oxidase Indicates That Certain Rhizobia Can Produce Bioactive Gibberellin A4, Ryan S. Nett, Tiffany Contreras, and Reuben J. Peters

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Elucidation of gibberellin biosynthesis in bacteria reveals convergent evolution, Ryan S. Nett, Mariana Montanares, Ariana Marcassa, Xuan Lu, Raimund Nagel, Trevor C. Charles, Peter Hedden, Maria Cecilia Rojas, and Reuben J. Peters

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Data on IL-10R neutralization-induced chronic colitis in Lipocalin 2 deficient mice on BALB/c background, Vishal Singh, Beng San Yeoh, Marit Nilsen-Hamilton, Thorsten Berger, Tak W. Mak, and Matam Vijay-Kumar

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Carbohydrate–Polypeptide Contacts in the Antibody Receptor CD16A Identified through Solution NMR Spectroscopy, Ganesh P. Subedi, Daniel J. Falconer, and Adam W. Barb

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Probing Labdane-Related Diterpenoid Biosynthesis in the Fungal Genus Aspergillus, Meimei Xu, Matthew L. Hillwig, Mollie S. Tiernan, and Reuben J. Peters

Submissions from 2016

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An encodable lanthanide binding tag with reduced size and flexibility for measuring residual dipolar couplings and pseudocontact shifts in large proteins, Adam W. Barb and Ganesh P. Subedi

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Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases, Nikita Chopra, Thomas E. Wales, Raji E. Joseph, Scott E. Boyken, John R. Engen, Robert L. Jernigan, and Amy H. Andreotti

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A tandem array of ent-kaurene synthases in maize with roles in gibberellin and more specialized metabolism, Jingye Fu, Fei Ren, Xuan Lu, Hongjie Mao, Meimei Xu, Jörg Degenhardt, Reuben J. Peters, and Qiang Wang

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Cytochrome P450 promiscuity leads to a bifurcating biosynthetic pathway for tanshinones, Juan Guo, Xiaohui Ma, Yuan Cai, Ying Ma, Zhilai Zhan, Yongjin J. Zhou, Wujun Liu, Mengxin Guan, Jian Yang, Guanghong Cui, Liping Kang, Lei Yang, Ye Shen, Jinfu Tang, Huixin Lin, Xiaojing Ma, Baolong Jin, Zhenming Liu, Reuben J. Peters, Zongbao K. Zhao, and Luqi Huang

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Aptamers in analytics, Muslum Ilgu and Marit Nilsen-Hamilton

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Extending a Single Residue Switch for Abbreviating Catalysis in Plant ent-Kaurene Synthases, Meirong Jia and Reuben J. Peters

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Extreme promiscuity of a bacterial and a plant diterpene synthase enables combinatorial biosynthesis, Meirong Jia, Kevin C. Potter, and Reuben J. Peters

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Investigating inducible short‐chain alcohol dehydrogenases/reductases clarifies rice oryzalexin biosynthesis, Naoki Kitaoka, Yisheng Wu, Jiachen Zi, and Reuben J. Peters

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Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha, Santosh Kumar, Chase Kempinski, Xun Zhuang, Ayla Norris, Sibongile Mafu, Jiachen Zi, Stephen A. Bell, Stephen Eric Nybo, Scott E. Kinison, Zuodong Jiang, Sheba Goklany, Kristin B. Linscott, Xinlu Chen, Qidong Jia, Shoshana D. Brown, John L. Bowman, Patricia C. Babbitt, Reuben J. Peters, Feng Chen, and Joe Chappell

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Direct Characterization of the Maize Starch Synthase IIa Product Shows Maltodextrin Elongation Occurs at the Non-reducing End, Mark E. Larson, Daniel J. Falconer, Alan M. Myers, and Adam W. Barb

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Fold-specific sequence scoring improves protein sequence matching, Sumudu P. Leelananda, Andrzej Kloczkowski, and Robert L. Jernigan

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Probing the promiscuity of ent-kaurene oxidases via combinatorial biosynthesis, Sibongile Mafu, Meirong Jia, Jiachen Zi, Dana Morrone, Yisheng Wu, Meimei Xu, Matthew L. Hillwig, and Reuben J. Peters

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Characterization of CYP71Z18 indicates a role in maize zealexin biosynthesis, Hongjie Mao, Jiang Liu, Fei Ren, Reuben J. Peters, and Qiang Wang

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A rapid fluorometric assay for the S-malonyltransacylase FabD and other sulfhydryl utilizing enzymes, Aaron M. Marcella and Adam W. Barb

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Labeling Studies Clarify the Committed Step in Bacterial Gibberellin Biosynthesis, Ryan S. Nett, Jeroen S. Dickschat, and Reuben J. Peters

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Product Rearrangement from Altering a Single Residue in the Rice syn-Copalyl Diphosphate Synthase, Kevin C. Potter, Meirong Jia, Young J. Hong, Dean Tantillo, and Reuben J. Peters

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Blocking Deprotonation with Retention of Aromaticity in a Plant ent-Copalyl Diphosphate Synthase Leads to Product Rearrangement, Kevin C. Potter, Jiachen Zi, Young J. Hong, Samuel Schulte, Brandi Malchow, Dean J. Tantillo, and Reuben J. Peters

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Distributions of experimental protein structures on coarse-grained free energy landscapes, Kannan Sankar, Jie Liu, Yuan Wang, and Robert L. Jernigan

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Digitor/dASCIZ Has Multiple Roles in Drosophila Development, Saheli Sengupta, Uttama Rath, Changfu Yao, Michael Zavortink, Chao Wang, Jack Girton, Kristen M. Johansen, and Jorgen Johansen

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Identification of a Dolabellane Type Diterpene Synthase and other Root-Expressed Diterpene Synthases in Arabidopsis, Qiang Wang, Meirong Jia, Jung-Hyun Huh, Andrew Muchlinski, Reuben J. Peters, and Dorothea Tholl

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Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza, Haibin Xu, Reuben J. Peters, and et al.

Submissions from 2015

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Functional Divergence of Diterpene Syntheses in the Medicinal Plant Salvia miltiorrhiza, Guanghong Cui, Lixin Duan, Baolong Jin, Jun Qian, Zheyong Xue, Guoan Shen, John Hugh Snyder, Jingyuan Song, Shilin Chen, Luqi Huang, Reuben J. Peters, and Xiaoquan Qi

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Scaffold Protein SLP-76 Primes PLCγ1 for Activation by ITK-Mediated Phosphorylation, Sujan Devkota, Raji E. Joseph, Lie Min, D. Bruce Fulton, and Amy Andreotti

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Combining Disparate Data Types: Protein Sequences and Protein Structures, Kejue Jia and Robert L. Jernigan

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Soybean Aphid Infestation Induces Changes in Fatty Acid Metabolism in Soybean, Charles Kanobe, Michael T. McCarville, Matthew E. O'Neal, Gregory L. Tylka, and Gustavo C. Macintosh

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The Use of Experimental Structures to Model Protein Dynamics, Ataur R. Katebi, Kannan Sankar, Kejue Jia, and Robert L. Jernigan

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Patterns of Metabolite Changes Identified from Large-Scale Gene Perturbations in Arabidopsis Using a Genome-Scale Metabolic Network, Taehyong Kim, Kate Dreher, Ricardo Nilo-Poyanco, Insuk Lee, Oliver Fiehn, Bernd Markus Lange, Basil J. Nikolau, Lloyd Sumner, Ruth Welti, Eve S. Wurtele, and Seung Y. Rhee

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The Application of Synthetic Biology to Elucidation of Plant Mono-, Sesqui-, and Diterpenoid Metabolism, Naoki Kitaoka, Xuan Lu, Bing Yang, and Reuben J. Peters

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Optimization of recombinant expression enables discovery of novel cytochrome P450 activity in rice diterpenoid biosynthesis, Naoki Kitaoka, Yisheng Wu, Meimei Xu, and Reuben J. Peters

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A systems biology approach toward understanding seed composition in soybean, Ling Li, Manhoi Hur, Joon-Yong Lee, Wenxu Zhou, Zhihong Song, Nick Ransom, Cumhur Yusuf Demirkale, Daniel S. Nettleton, Mark E. Westgate, Zebulun Wayne Arendsee, Vidya Vaancheeswaran Iyer, Jacqueline V. Shanks, Basil Nikolau, and Eve Wurtele

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Cell wall traits as potential resources to improve resistance of durum wheat against Fusarium graminearum, Vincenzo Lionetti, Angelica Giancaspro, Eleonora Fabri, Stefania L. Giove, Nathan Reem, Olga A. Zabotina, Antonio Blanco, Agata Gadaleta, and Daniela Bellincampi

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Effect of Surface Hydrophobicity on the Function of the Immobilized Biomineralization Protein Mms6, Xunpei Liu, Honghu Zhang, Srikanth Nayak, German Parada, James W. Anderegg, Shuren Feng, Marit Nilsen-Hamilton, Mufit Akinc, and Surya K. Mallapragada

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Efficient heterocyclisation by (di)terpene synthases, S. Mafu, K. C. Potter, M. L. Hillwig, S. Schulte, J. Criswell, and R. J. Peters

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Biosynthesis of the Diterpenoid Lycosantalonol via Nerylneryl Diphosphate in Solanum lycopersicum, Yuki Matsuba, Jiachen Zi, A. Daniel Jones, Reuben J. Peters, and Eran Pichersky

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Crystallization and preliminary X-ray analysis of the Plasmodium falciparum apicoplast DNA polymerase, Morgan Eilise Milton, Jun-yong Choe, Richard B. Honzatko, and Scott W. Nelson

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Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models, Hyuntae Na, Robert L. Jernigan, and Guang Song

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Metabolomic Profiling of the Nectars of Aquilegia pubescens and A. Canadensis, Christos Noutsos, Ann Perera, Basil Nikolau, Samuel M.D. Seaver, and Doreen Ware

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High Yield Expression of Recombinant Human Proteins with the Transient Transfection of HEK293 Cells in Suspension, Ganesh P. Subedi, Roy W. Johnson, Heather A. Moniz, Kelley W. Moreman, and Adam W. Barb

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CRISPR interference and priming varies with individual spacer sequences, Chaoyou Xue, Arun S. Seetharam, Olga Musharova, Konstantin Severinov, Stan J. J. Brouns, Andrew J. Severin, and Dipali G. Sashital