SelectedWorks - Robert Jernigan

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Selected Works of Robert Jernigan

Professor of Biochemistry, Biophysics and Molecular Biology

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About Robert Jernigan

Present	Professor of Biochemistry, Biophysics and Molecular Biology, Iowa State University
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Biochemistry, Biophysics, and Structural Biology

Articles (203)

Non-Coding RNA in Raw and Commercially Processed Milk and Putative ...

Food Science and Human Nutrition Publications (2020)

Sayane Shome, Robert Jernigan, Donald C. Beitz, Stephanie Clark, et al.

Background: Bovine milk contains extracellular vesicles (EVs) that play a role in cellular communication, acting in either an autocrine, paracrine, ...

Characterizing and Predicting Protein Hinges for Mechanistic Insight

Journal of Molecular Biology (2019)

Pranav M. Khade, Ambuj Kumar and Robert L. Jernigan

The functioning of proteins requires highly specific dynamics, which depend critically on the details of how amino acids are packed. ...

Combinatorial biosynthesis and the basis for substrate promiscuity in class ...

Metabolic Engineering (2019)

Meirong Jia, Sambit K. Mishra, Samuel Tufts, Robert L. Jernigan, et al.

Terpene synthases are capable of mediating complex reactions, but fundamentally simply catalyze lysis of allylic diphosphate esters with subsequent deprotonation. ...

Coupling Dynamics and Evolutionary Information with Structure to Identify Protein ...

Proteins (2019)

Sambit Kumar Mishra, Gaurav Kandoi and Robert L. Jernigan

Binding sites in proteins can be either specifically functional binding sites (active sites) that bind specific substrates with high affinity ...

Entropy, Fluctuations, and Disordered Proteins

Eshel Faraggi, A. Keith Dunker, Robert L. Jernigan and Andrzej Kloczkowski

Entropy should directly reflect the extent of disorder in proteins. By clustering structurally related proteins and studying the multiple-sequence-alignment of ...

Protein dynamic communities from elastic network models align closely to ...

PloS ONE (2018)

Sambit Kumar Mishra and Robert L. Jernigan

Dynamic communities in proteins comprise the cohesive structural units that individually exhibit rigid body motions. These can correspond to structural ...

SeqStruct : A New Amino Acid Similarity Matrix Based on Sequence ...

Kejue Jia and Robert L. Jernigan

Protein sequence matching does not properly account for some well-known features of protein structures: surface residues being more variable than ...

Comparisons of Protein Dynamics from Experimental Structure Ensembles, Molecular Dynamics ...

The Journal of Physical Chemistry B (2018)

Kannan Sankar, Sambit K. Mishra and Robert L. Jernigan

Predicting protein motions is important for bridging the gap between protein structure and function. With growing numbers of structures of ...

Altered dynamics upon oligomerization corresponds to key functional sites

Proteins: Structure, Function, and Bioinformatics (2017)

Sambit Kumar Mishra, Kannan Sankar and Robert L. Jernigan

It is known that over half of the proteins encoded by most organisms function as oligomeric complexes. Oligomerization confers structural ...

Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec ...

PLOS Computational Biology (2016)

Nikita Chopra, Thomas E. Wales, Raji E. Joseph, Scott E. Boyken, et al.

Bruton’s tyrosine kinase (Btk) is a Tec family non-receptor tyrosine kinase that plays a critical role in immune signaling and ...

Ribosome Mechanics Informs about Mechanism

Journal of Molecular Biology (2016)

Michael T. Zimmermann, Kejue Jia and Robert L. Jernigan

The essential aspects of the ribosome’s mechanism can be extracted from coarse-grained simulations, including the ratchet motion, the movement together ...

Distributions of experimental protein structures on coarse-grained free energy landscapes

The Journal of Chemical Physics (2016)

Kannan Sankar, Jie Liu, Yuan Wang and Robert L. Jernigan

Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available ...

Fold-specific sequence scoring improves protein sequence matching

BMC Bioinformatics (2016)

Sumudu P. Leelananda, Andrzej Kloczkowski and Robert L. Jernigan

Background Sequence matching is extremely important for applications throughout biology, particularly for discovering information such as functional and evolutionary relationships, ...

Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy ...

PLOS Computational Biology (2015)

Hyuntae Na, Robert L. Jernigan and Guang Song

Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as ...

Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics

Biochemistry (2015)

Ataur R. Katebi and Robert L. Jernigan

Aldolases are essential enzymes in the glycolysis pathway and catalyze the reaction cleaving fructose/tagatose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde ...

ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity ...

Infection and Immunity (2015)

Fengwei Jiang, Chunxia An, Yinli Bao, Xuefeng Zhao, et al.

Avian pathogenic Escherichia coli (APEC) strains cause one of the three most significant infectious diseases in the poultry industry and ...

Combining Disparate Data Types: Protein Sequences and Protein Structures

Journal of Data Mining in Genomics & Proteomics (2015)

Kejue Jia and Robert L. Jernigan

With the development of high-throughput, next-generation sequencing and other advanced technologies, a large number of gene expression profiles have been ...

A conserved isoleucine maintains the inactive state of Bruton’s ...

Journal of Molecular Biology (2014)

Scott E. Boyken, Nikita Chopra, Qian Xie, Raji E. Joseph, et al.

Despite high homology among non-receptor tyrosine kinases, different kinase families employ a diverse array of regulatory mechanisms. For example, the ...

Computational and Experimental Characterization of RNA Cubic Nanoscaffolds

Kirill A Afonin, Wojciech K Kasprzak, Eckart Bindewald, Praneet S Puppala, et al.

The fast-developing field of RNA nanotechnology requires the adoption and development of novel and faster computational approaches to modeling and ...

Factors correlating with significant differences between X-ray structures of myoglobin

Acta Crystallographica Section D (2014)

Alexander A Rashin, Marcin J Domagalski, Michael T Zimmermann, Wladek Minor, et al.

Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful ...

Elastic network models capture the motions apparent within ensembles of ...

Michael T. Zimmermann and Robert L. Jernigan

The role of structure and dynamics in mechanisms for RNA becomes increasingly important. Computational approaches using simple dynamics models have ...

Distributions of amino acids suggest that certain residue types more ...

Journal of Molecular Modeling (2013)

S. Saraswathi Battelle, J .L. Fernández-Martínez, A. Koliński, R. L. Jernigan, et al.

Exponential growth in the number of available protein sequences is unmatched by the slower growth in the number of structures. ...

Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model ...

Bulletin of Mathematical Biology (2013)

Jun-Koo Park, Robert Jernigan and Zhijun Wu

We investigate several approaches to coarse grained normal mode analysis on protein residual-level structural fluctuations by choosing different ways of ...

Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure ...

Journal of Molecular Modeling (2012)

Saras Saraswathi, Juan Luis Fernandez-Martinez, Andrzej Kolinski, Robert L. Jernigan, et al.

Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome ...

P.R.E.S.S. – An R-package for Exploring Residual-Level ...

Journal of Bioinformatics and Computational Biology (2012)

Yuanyuan Huang, Steve Bonett, Andrzej Klockowski, Robert Jernigan, et al.

P.R.E.S.S. is an R package developed to allow researchers to get access to and manipulate on a large set of ...