James R. Cox

Probing Phenylalanine/Adenine π-Stacking Interactions in Protein Complexes with Explicitly Correlated and CCSD(T) Computations

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.

Audio Podcasting in a Tablet PC-Enhanced Biochemistry Course.

This report describes the effects of making audio podcasts of all lectures in a large, basic biochemistry course promptly available to students. The audio podcasts complement a previously described approach in which a tablet PC is used to annotate PowerPoint slides with digital ink to produce electronic notes that can be archived. The fundamentals of this approach are described, and data from student attitudinal and informational surveys are presented. The survey data suggest that the students have a positive attitude toward the combination of tablet‐based instruction and audio podcasting. In addition, three students provide testimonials on how these technological tools allowed them to utilize their preferred learning styles to succeed in the course. Possible negative consequences of this approach, in terms of class attendance and note taking, are also analyzed and discussed.

Examination of tyrosine/adenine stacking interactions in protein complexes.

The π-stacking interactions between tyrosine amino acid side chains and adenine-bearing ligands are examined. Crystalline protein structures from the protein data bank (PDB) exhibiting face-to-face tyrosine/adenine arrangements were used to construct 20 unique 4-methylphenol/N9-methyladenine (p-cresol/9MeA) model systems. Full geometry optimization of the 20 crystal structures with the M06-2X density functional theory method identified 11 unique low-energy conformations. CCSD(T) complete basis set (CBS) limit interaction energies were estimated for all of the structures to determine the magnitude of the interaction between the two ring systems. CCSD(T) computations with double-ζ basis sets (e.g., 6-31G*(0.25) and aug-cc-pVDZ) indicate that the MP2 method overbinds by as much as 3.07 kcal mol(-1) for the crystal structures and 3.90 kcal mol(-1) for the optimized structures. In the 20 crystal structures, the estimated CCSD(T) CBS limit interaction energy ranges from -4.00 to -6.83 kcal mol(-1), with an average interaction energy of -5.47 kcal mol(-1), values remarkably similar to the corresponding data for phenylalanine/adenine stacking interactions. Geometry optimization significantly increases the interaction energies of the p-cresol/9MeA model systems. The average estimated CCSD(T) CBS limit interaction energy of the 11 optimized structures is 3.23 kcal mol(-1) larger than that for the 20 crystal structures.

Enhancing student interactions with the instructor and content using pen-based technology, YouTube videos, and virtual conferencing.

This report describes the incorporation of digital learning elements in organic chemistry and biochemistry courses. The first example is the use of pen‐based technology and a large‐format PowerPoint slide to construct a map that integrates various metabolic pathways and control points. Students can use this map to visualize the integrated nature of metabolism and how various hormones impact metabolic regulation. The second example is the embedding of health‐related YouTube videos directly into PowerPoint presentations. These videos become a part of the course notes and can be viewed within PowerPoint as long as students are online. The third example is the use of a webcam to show physical models during online sessions using web‐conferencing software. Various molecular conformations can be shown through the webcam, and snapshots of important conformations can be incorporated into the notes for further discussion and annotation. Each of the digital learning elements discussed in this report is an attempt to use technology to improve the quality of educational resources available outside of the classroom to foster student engagement with ideas and concepts. Biochemistry and Molecular Biology Education Vol. 39, No. 1, pp. 4–9, 2011

Virtual office hours using a tablet PC: E-lluminating biochemistry in an online environment

The availability of online collaboration software has provided new opportunities for instructors to interact with students outside the classroom. This report describes how Elluminate Live!®, a particular conferencing software package, can be used with a tablet PC to conduct virtual office hours in a biochemistry course. The educational value of engaging students in an online environment, with text messaging, voice‐over‐internet protocol (VoIP), and application sharing is also discussed. A student perspective is provided to illustrate the advantages of conducting virtual office hours and how the combination of online collaboration software and tablet PC technology can provide an enhanced learning experience.

Lesson plan for protein exploration in a large biochemistry class

The teaching of structural concepts plays a prominent role in many chemistry and biology courses. When it comes to macromolecular systems, a thorough understanding of noncovalent interactions lays a strong foundation for students to understand such things as protein folding, the formation of protein‐ligand complexes, and the melting of the DNA double helix. The incorporation of computer‐based molecular graphics into the biochemistry curriculum has given students unique opportunities in visualizing the structure of biological molecules and recognizing the subtle aspects of noncovalent interactions. This report describes a series of visualization‐based assignments developed to facilitate protein exploration in a large biochemistry class. A large enrollment can present special challenges for students to benefit from hands‐on use of visualization software. Three of the assignments are described in detail along with a description of an on‐line teaching tool used to manage the assignments and to coordinate the student groups participating in these exercises.

Screen Capture on the Fly: Combining Molecular Visualization and a Tablet PC in the Biochemistry Lecture

The biochemistry lecture is often the place where students receive the greatest exposure to the structural nature of biomolecules. The use of molecular visualization software and web‐based animated tutorials has enhanced the way instructors teach this important area of structural biology. Using the software and tutorials in class is an excellent way to teach the diverse structural motifs found in biomolecules; however, integrating the computer‐based molecular renderings shown in class into lecture notes is challenging. This report describes how incorporating a tablet PC into the biochemistry lecture can be used in conjunction with molecular visualization software to create a rich set of lecture notes. The pedagogical tools associated with a tablet PC make it an attractive addition to the biochemistry lecture, which usually has significant audio and visual learning components.

TEACHING THE STRUCTURAL NATURE OF BIOLOGICAL MOLECULES: MOLECULAR VISUALIZATION IN THE CLASSROOM AND IN THE HANDS OF STUDENTS

The use of molecular visualization software has made a tremendous impact in the biochemistry and cell biology classroom. Instructors no longer have to rely on static images in textbooks to teach the structural nature of biological molecules. The emergence of many different molecular graphics programs and technology-based classrooms has enhanced the ability of instructors to teach structural concepts such as noncovalent interactions and levels of organization in proteins. Many web-based tutorials are also available for instructors to use during lecture or for students to explore outside of the classroom. Students can also obtain hands-on experience with the graphics programs to explore the structural aspects of macromolecular systems. This report shows that students involved in visualization projects become skilled at identifying various structural motifs they have discussed in class or are discovering for the first time. This student-centered approach enhances the ability of students to comprehend structural concepts and to realize the importance of weak interactions in the structure of large molecules. [Chem. Educ. Res. Pract. Eur.: 2001, 2, 109-122]

Aminoglycoside antibiotics bound to aminoglycoside-detoxifying enzymes and RNA adopt similar conformations.

Conformations of ribostamycin and isepamicin, aminoglycoside antibiotics, bound to an aminoglycoside antibiotic, 3′-phosphotransferase, were determined by transferred nuclear Overhauser effect spectroscopy and molecular modeling. Two major conformers of enzyme-bound ribostamycin, a neomycin-group aminoglyeoside were observed. The 3′- and 5″-OH groups (reactive hydroxyl groups) in the conformers are placed in approximate locations. One of the conformers is similar to the structure of paromomycin bound to a 27-nucleotide piece of ribosomal RNA that represents the A-site of the small ribosomal subunit, where rings A and C are in an orthogonal arrangement.Isepamicin, a kanamycin-group aminoglycoside antibiotic, also showed two major enzyme-bound conformations. Both conformations were similar to those observed for bound isepamicin in the active site of an aminoglycoside(6′)-acetyl transferase-Ii. Conformations of other RNA-bound kanamycin-group aminoglycosides were also similar to the enzyme-bound conformations of isepamicin. These observations suggest that aminoglycosides may adopt similar conformations when bound to RNA and protein targets. This may have significant implications in the design of enzyme inhibitors and/or antibiotics.

Combining content and elements of communication into an upper‐level biochemistry course

This report describes how a science communication module was incorporated into an advanced biochemistry course. Elements of communication were taught synergistically with biochemistry content in this course in an effort to expose students to a variety of effective oral communication strategies. Students were trained to use these established techniques and incorporated them into various presentations throughout the course. Three students describe their use of specific resources and how the skills learned relate to their future career. The importance and relevance of science communication are receiving unprecedented national attention. The academic scientific community must respond by incorporating more communication‐centered instruction and opportunities in the classroom and laboratory.