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

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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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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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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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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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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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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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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Investigating the Phylogenetic Range of Gibberellin Biosynthesis in Bacteria, Raimund Nagel 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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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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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

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

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Morphological Transformations in the Magnetite Biomineralizing Protein Mms6 in Iron Solutions: A Small-Angle X-ray Scattering Study, Honghu Zhang, Xunpei Liu, Shuren Feng, Wenjie Wang, Klaus Schmidt-Rohr, Mufit Akinc, Marit Nilsen-Hamilton, David Vaknin, and Surya K. Mallapragada

Submissions from 2014

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Computational and Experimental Characterization of RNA Cubic Nanoscaffolds, Kirill A. Afonin, Wojciech K. Kasprzak, Eckart Bindewald, Praneet S. Puppala, Alex R. Diehl, Kenneth T. Hall, Tae Jin Kim, Michael T. Zimmermann, Robert L. Jernigan, Luc Jaeger, and Bruce A. Shapiro

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Phylogenetic Analyses and Characterization of RNase X25 from Drosophila melanogaster Suggest a Conserved Housekeeping Role and Additional Functions for RNase T2 Enzymes in Protostomes, Linda Ambrosio, Stephanie Morriss, Ayesha Riaz, Ryan Bailey, Jian Ding, and Gustavo C. Macintosh

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Solubility of Recombinant Src Homology 2 Domains Expressed in E. coli Can Be Predicted by TANGO, Thorny Cecilie Bie Andersen, Kjersti Kjersti Lindsjø, Cecilie Dahl Hem, Lise Koll, Per Eugen Kristiansen, Lars Skjeldal, Amy H. Andreotti, and Anne Spurkland

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A conserved isoleucine maintains the inactive state of Bruton’s tyrosine kinase, Scott E. Boyken, Nikita Chopra, Qian Xie, Raji E. Joseph, Thomas E. Wales, D. Bruce Fulton, John R. Engen, Robert L. Jernigan, and Amy H. Andreotti

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Genome-wide analysis of regulation of gene expression and H3K9me2 distribution by JIL-1 kinase mediated histone H3S10 phosphorylation in Drosophila, Weili Cai, Chao Wang, Yeran Li, Changfu Yao, Lu Shen, Sanzhen Liu, Xiaomin Bao, Patrick S. Schnable, Jack Girton, Jorgen Johansen, and Kristen M. Johansen

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Combining Metabolomics and Transcriptomics to Characterize Tanshinone Biosynthesis in Salvia Miltiorrhiza, Wei Gao, Hai-Xi Sun, Guanghong Cui, Matthew L. Hillwig, Alana Jackson, Xiao Wang, Ye Shen, Liangxiao Zhang, Xiu-Jie Wang, Reuben J. Peters, and Luqi Huang

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Autoinhibition of Bacteriophage T4 Mre11 by Its C-terminal Domain, Yang Gao and Scott Nelson

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Catalytic Mechanism of Bacteriophage T4 Rad50 ATP Hydrolysis, Timothy J. Herdendorf and Scott W. Nelson

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Functional Conservation of the Capacity for ent-Kaurene Biosynthesis and an Associated Operon in Certain Rhizobia, David M. Hershey, Xuan Lu, Jiachen Zi, and Reuben J. Peters

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An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures, Muslum Ilgu, D. Bruce Fulton, Ragothaman M. Yennamalli, Monica H. Lamm, Taner Z. Sen, and Marit Nilsen-Hamilton

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Biochemical characterization of the castor bean ent-kaurene synthase(-like) family supports quantum chemical view of diterpene cyclization, Alana J. Jackson, David M. Hershey, Taylor Chesnut, Meimei Xu, and Reuben J. Peters

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Evaluating PHA Productivity of Bioengineered Rhodosprillum rubrum, Huanan Jin and Basil Nikolau

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1.55 Å-resolution structure of ent-copalyl diphosphate synthase and exploration of general acid function by site-directed mutagenesis, Mustafa Köksal, Kevin Potter, Reuben J. Peters, and David W. Christianson

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Factors correlating with significant differences between X-ray structures of myoglobin, Alexander A. Rashin, Marcin J. Domagalski, Michael T. Zimmermann, Wladek Minor, Maksymilian Chruszcz, and Robert L. Jernigan

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Biosynthesis, elicitation and roles of monocot terpenoid phytoalexins, Eric A. Schmelz, Alisa Huffaker, James W. Sims, Shawn A. Christensen, Xuan Lu, Kuzunori Okada, and Reuben J. Peters

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Live-cell imaging of Pol II promoter activity to monitor gene expression with RNA IMAGEtag reporters, Ilchung Shin, Judhajeet Ray, Vinayak Gupta, Muslum Ilgu, Jonathan Scott Beasley, Lee Bendickson, Samir Mehanovic, George A. Kraus, and Marit Nilsen-Hamilton

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Histone H3S10 phosphorylation by the JIL-1 kinase in pericentric heterochromatin and on the fourth chromosome creates a composite H3S10phK9me2 epigenetic mark, Chao Wang, Yeran Li, Weili Cai, Xiaomin Bao, Jack Girton, Jorgen Johansen, and Kristen M. Johansen

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Calmodulin and PI(3,4,5)P3 cooperatively bind to the Itk pleckstrin homology domain to promote efficient calcium signaling and IL-17A production, Xinxin Wang, Scott E. Boyken, Jiancheng Hu, Xiaolu Xu, Ryan P. Rimer, Madeline A. Shea, Andrey S. Shaw, Amy H. Andreotti, and Yina H. Huang

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A Selective NMR Probe to Monitor the Conformational Transition from Inactive to Active Kinase, Qian Xie, D. Bruce Fulton, and Amy H. Andreotti

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Characterization of an Orphan Diterpenoid Biosynthetic Operon from Salinispora arenicola, Meimei Xu, Matthew L. Hillwig, Amy L. Lane, Mollie Tiernan, Bradley S. Moore, and Reuben J. Peters

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The Spindle Matrix Protein, Chromator, Is a Novel Tubulin Binding Protein That Can Interact with Both Microtubules and Free Tubulin, Changfu Yao, Chao Wang, Yeran Li, Yun Ding, Uttama Rath, Saheli Sengupta, Jack Girton, Kristen M. Johansen, and Jorgen Johansen

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Biosynthesis of Lycosantalonol, a cis-Prenyl Derived Diterpenoid, Jiachen Zi, Yuki Matsuba, Young J. Hong, Alana Jackson, Dean J. Tantillo, Eran Pichersky, and Reuben J. Peters

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Elastic network models capture the motions apparent within ensembles of RNA structures, Michael T. Zimmermann and Robert L. Jernigan

Submissions from 2013

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Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure, S. Saraswathi Battelle, J .L. Fernández-Martínez, A. Koliński, R. L. Jernigan, and A. Kloczkowski Battelle

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Integrated Self-Assembly of the Mms6 Magnetosome Protein to Form an Iron-Responsive Structure, Shuren Feng, Lijun Wang, Pierre E. Palo, Xunpei Liu, Surya K. Mallapragada, and Marit Nilsen-Hamilton

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The effect of JIL-1 on position-effect variegation is proportional to the total amount of heterochromatin in the genome, Jack Girton, Chao Wang, Jorgen Johansen, and Kristen M. Johansen

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Activation Loop Dynamics Determine the Different Catalytic Efficiencies of B Cell– and T Cell–Specific Tec Kinases, Raji E. Joseph, Iivari Kleino, Thomas E. Wales, Qian Xie, D. Bruce Fulton, John R. Engen, Leslie J. Berg, and Amy H. Andreotti

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Domain Requirements of the JIL-1 Tandem Kinase for Histone H3 Serine 10 Phosphorylation and Chromatin Remodeling in Vivo, Yeran Li, Weili Cai, Chao Wang, Changfu Yao, Xiaomin Bao, Huai Deng, Jack Girton, Jorgen Johansen, and Kristen M. Johansen

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Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model for Protein Residue-Level Structural Fluctuations, Jun-Koo Park, Robert Jernigan, and Zhijun Wu

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Evidence against a Role for the JIL-1 Kinase in H3S28 Phosphorylation and 14-3-3 Recruitment to Active Genes in Drosophila, Chao Wang, Changfu Yao, Yeran Li, Weili Cai, Xiaomin Bao, Jack Girton, Jorgen Johansen, and Kristen M. Johansen

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Fidelity, Mismatch Extension, and Proofreading Activity of the Plasmodium falciparum Apicoplast DNA Polymerase, Bentley Wingert, Eric Evan Parrott, and Scott W. Nelson