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Cataract disease is strongly associated with progressively accumulating oxidative damage to the extremely long-lived crystallin proteins of the lens. Cysteine oxidation affects crystallin folding, interactions, and light-scattering aggregation especially strongly due to the formation of disulfide bridges. Minimizing crystallin aggregation is crucial for lifelong lens transparency, so one might expect the ubiquitous lens crystallin superfamilies (α and βγ) to contain little cysteine. Yet, the Cys content of γ-crystallins is well above the average for human proteins. We review literature relevant to this longstanding puzzle and take advantage of expanding genomic databases and improved machine learning tools for protein structure prediction to investigate it further. We observe remarkably low Cys conservation in the βγ-crystallin superfamily; however, in γ-crystallin, the spatial positioning of Cys residues is clearly fine-tuned by evolution. We propose that the requirements of long-term lens transparency and high lens optical power impose competing evolutionary pressures on lens βγ-crystallins, leading to distinct adaptations: high Cys content in γ-crystallins but low in βB-crystallins. Aquatic species need more powerful lenses than terrestrial ones, which explains the high methionine content of many fish γ- (and even β-) crystallins. Finally, we discuss synergies between sulfur-containing and aromatic residues in crystallins and suggest future experimental directions. 

ABSTRACT Specifications grading is a student-centered assessment method that enables flexibility and opportunities for revision. Here, we describe the first known full implementation of specifications grading in an upper-division chemical biology course. Due to the rapid development of relevant knowledge in this discipline, the overarching goal of this class is to prepare students to interpret and communicate about current research. In the past, a conventional points-based assessment method made it challenging to ensure that satisfactory standards for student work were consistently met, particularly for comprehensive written assignments. Specifications grading was chosen because the core tenet requires students to demonstrate minimum learning objectives to achieve a passing grade and complete more content of increased cognitive complexity to achieve higher grades. This strict adherence to determining grades based on demonstrated skills is balanced by opportunities for revision or flexibility in assignment deadlines. These options are made manageable for the instructors through the use of a token economy with a limited number of tokens that students can choose to use when needed. Over the duration of the course, a validated survey on self-efficacy showed slight positive trends, student comprehension and demonstrated skills qualitatively improved, and final grade distributions were not negatively affected. Instructors noticed that discussions with students were more focused on course concepts and feedback, rather than grades, while overall grading time was reduced. Responses to university-administered student feedback surveys revealed some self-reported reduction in anxiety, as well as increased confidence in managing time and course material. Recommendations are provided on how to continue to improve the overall teaching and learning experience for both instructors and students. 

ABSTRACT A major challenge for science educators is teaching foundational concepts while introducing their students to current research. Here we describe an active learning module developed to teach protein structure fundamentals while supporting ongoing research in enzyme discovery. It can be readily implemented in both entry-level and upper-division college biochemistry or biophysics courses. Preactivity lectures introduced fundamentals of protein secondary structure and provided context for the research projects, and a homework assignment familiarized students with 3-dimensional visualization of biomolecules with UCSF Chimera, a free protein structure viewer. The activity is an online survey in which students compare structure elements in papain, a well-characterized cysteine protease from Carica papaya, to novel homologous proteases identified from the genomes of an extremophilic microbe (Halanaerobium praevalens) and 2 carnivorous plants (Drosera capensis and Cephalotus follicularis). Students were then able to identify, with varying levels of accuracy, a number of structural features in cysteine proteases that could expedite the identification of novel or biochemically interesting cysteine proteases for experimental validation in a university laboratory. Student responses to a postactivity survey were largely positive and constructive, describing points in the activity that could be improved and indicating that the activity was an engaging way to learn about protein structure.