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Active Learning Module for Protein Structure Analysis Using Novel Enzymes
Jessica I. Kelz,
Gemma R. Takahashi,
Fatemeh Safizadeh,
Vesta Farahmand,
Marquise G. Crosby,
Jose L. Uribe,
Suhn H. Kim,
Marc A. Sprague-Piercy,
Elizabeth M. Diessner,
Brenna Norton-Baker,
Steven M. Damo,
Rachel W. Martin, and
Pavan Kadandale
Article Category: Research Article
Volume/Issue: Volume 3: Issue 1
Online Publication Date: Apr 06, 2022
DOI: 10.35459/tbp.2021.000209
Page Range: 49 – 63

, improved nuclear magnetic resonance instrumentation, and the “resolution revolution” in cryogenic electron microscopy have greatly accelerated the pace of protein structure determination studies. As this methodology becomes easier to use, familiarity with protein structures has become an essential competency needed for many types of biological research. Being able to visualize the relevant molecular structures improves mechanistic understanding of enzyme activity, protein–protein interactions, and regulation of biological processes such as transcription and translation

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Jon-Marc G. Rodriguez and
Marcy H. Towns
Article Category: Research Article
Volume/Issue: Volume 1: Issue 2
Online Publication Date: Apr 14, 2020
Page Range:

chemistry education research carried out in upper-division contexts on advanced topics. However, most work has still been contextualized in general chemistry courses, suggesting the need for more research that provides insight regarding how to enhance and improve the teaching and learning of advanced topics in the chemistry curriculum ( 23 , 24 ). In particular, chemical kinetics and enzyme kinetics have been identified as under-studied topics in the growing body of education literature ( 1 ). A review of the literature reveals a large library of resources to help

Fig 8; Students learn about rate laws and reaction order in general chemistry; in biochemistry, connections should be drawn between these ideas and enzyme kinetics.
Jon-Marc G. Rodriguez and
Marcy H. Towns
Fig 8
Fig 8

Students learn about rate laws and reaction order in general chemistry; in biochemistry, connections should be drawn between these ideas and enzyme kinetics.


Jon-Marc G. Rodriguez and
Marcy H. Towns
Fig 5
Fig 5

Enzyme inhibition can be framed as a spectrum with competitive, noncompetitive, and uncompetitive being special points on this continuum; figure reproduced from Rodriguez and Towns (69) with permission from the Royal Society of Chemistry.


Jessica I. Kelz,
Gemma R. Takahashi,
Fatemeh Safizadeh,
Vesta Farahmand,
Marquise G. Crosby,
Jose L. Uribe,
Suhn H. Kim,
Marc A. Sprague-Piercy,
Elizabeth M. Diessner,
Brenna Norton-Baker,
Steven M. Damo,
Rachel W. Martin, and
Pavan Kadandale
<bold>Fig 1</bold>
Fig 1

Papain secondary structure examples presented in presurvey lecture. (A) All α-helices (red) displayed as ribbons. (B) One α-helix (red) displayed with all atoms shown as stick models. (C) All β-strands (blue) displayed as ribbons. (D) Two β-strands (blue) displayed with all atoms shown as stick models.


Jessica I. Kelz,
Gemma R. Takahashi,
Fatemeh Safizadeh,
Vesta Farahmand,
Marquise G. Crosby,
Jose L. Uribe,
Suhn H. Kim,
Marc A. Sprague-Piercy,
Elizabeth M. Diessner,
Brenna Norton-Baker,
Steven M. Damo,
Rachel W. Martin, and
Pavan Kadandale
<bold>Fig 3</bold>
Fig 3

Comparison of the reference papain structure to a molecular model of a new protein, DCAP_4793. (A) The papain structure is shown in red. Circled areas (cyan) highlight differences in compared with DCAP_4793. (B) The molecular model for DCAP_4793, generated with Rosetta, is shown in blue. (C) An overlay of the 2 proteins in panels A and B highlights similarities and differences described in the main text. The active site residues in both proteins are shown as space-filling models with color codes as follows: cysteine, gold/yellow; histidine. purple/magenta; asparagine, dark/lime green for papain and DCAP_4793, respectively.


Jessica I. Kelz,
Gemma R. Takahashi,
Fatemeh Safizadeh,
Vesta Farahmand,
Marquise G. Crosby,
Jose L. Uribe,
Suhn H. Kim,
Marc A. Sprague-Piercy,
Elizabeth M. Diessner,
Brenna Norton-Baker,
Steven M. Damo,
Rachel W. Martin, and
Pavan Kadandale
<bold>Fig 2</bold>
Fig 2

Example cysteine proteases, aligned with papain (red), presented to students before taking the in-class survey. (A) Aspain: DCAP_3968 (orange). Aspain's unusual active site (top inset) replaces the typical asparagine (dark green) of papain (bottom inset) with aspartic acid (lime green). Its occluding loop, which partially blocks the active site, is indicated by an arrow. Other active site residues: cysteine, gold/yellow; histidine, purple/magenta for papain and aspain, respectively. (B) DCAP_6097 (dark grey). DCAP_6097's C-terminal granulin domain, indicated by an arrow, extends well beyond the rest of the papain-aligned structure.


Jessica I. Kelz,
Gemma R. Takahashi,
Fatemeh Safizadeh,
Vesta Farahmand,
Marquise G. Crosby,
Jose L. Uribe,
Suhn H. Kim,
Marc A. Sprague-Piercy,
Elizabeth M. Diessner,
Brenna Norton-Baker,
Steven M. Damo,
Rachel W. Martin, and
Pavan Kadandale
<bold>Fig 4</bold>
Fig 4

Example survey questions and student responses using proteins aligned to papain (red). (A) Examples of accurate and informative student responses using DCAP_5945 (light grey). (B) Example of ambiguity in student responses with DCAP_6547 (black). (C) Example of inaccuracy in student responses with C. follicularis protein A0A1Q3AYB2 (dark grey). (D) Accuracy of all student responses to Q3, Q4.5, and Q13. All 34 proteins are shown in each panel, and those whose examples appear in panels A, B, and C are indicated by colored stars (DCAP_5945, light grey; DCAP_6547, black; A0A1Q3AYB2, dark grey). Black brackets below each graph show which subsets of proteins contain the feature in question.


G. Zifarelli,
P. Zuccolini,
S. Bertelli, and
M. Pusch
Fig 1
Fig 1

Principles of enzyme and ion channel function. In (A) the cartoon depicts the reaction steps of a hypothetical enzyme that binds a substrate, cuts it, and then releases 2 products. (B) Single-channel traces of an acetylcholine receptor at various voltages are shown (4). (C) This illustrates the typical dwell-time distributions of a 3-state system with 2 closed states and 1 open state, in which the open dwell-time distribution is well fitted by a single exponential function (left, pink line), while the closed state histogram requires the sum of 2 exponential functions (right, pink line). The histograms were generated by MarkovEditor and a simple 3-state system. (D) All examples of Markov models are explained in more detail in the present article.


Constance J. Jeffery
Article Category: Brief Report
Volume/Issue: Volume 2: Issue 2
Online Publication Date: Jun 29, 2021
Page Range: 23 – 27

analysis. The graduate students expanded and updated that architecture of the database to provide sections for the new types of information. The professor checked all of the work and uploaded it into the online database with the help of the graduate students. As part of the training, all the students started by reading review articles about moonlighting proteins ( 2 , 6 ), followed by a paper about the human angiotensin-converting enzyme 2 (ACE2) protein and preparing a practice annotation for that protein that we could go over