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The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.

The computer game Foldit is currently widely used as a biology and biochemistry teaching aid. Herein, we introduce a new feature of Foldit called "custom contests" that allows educators to create puzzles that fit their curriculum. The effectiveness of the custom contests is demonstrated by the use of five distinct custom contests in an upper-level biochemistry class. The new custom contest feature can be implemented in classes ranging from middle school to graduate school to enable educators to best complement their current curriculum.

Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone.

How nucleic acids interact with proteins, and how they affect protein folding, aggregation, and misfolding is a still‐evolving area of research. Considerable effort is now focusing on a particular structure of RNA and DNA, G‐quadruplexes, and their role in protein homeostasis and disease. In this state‐of‐the‐art review, we track recent reports on how G‐quadruplexes influence protein aggregation, proteolysis, phase separation, and protein misfolding diseases, and pose currently unanswered questions in the advance of this scientific field. [ABSTRACT FROM AUTHOR]

Recently, 57 undergraduate students at the University of Michigan were assigned the task of solving a crystal structure, given only the electron density map of a 1.3 Å crystal structure from the electron density server, and the position of the N-terminal amino acid. To test their knowledge of amino acid chemistry, the students were not given the protein sequence. With minimal direction from the instructor on how the students should complete the assignment, the students fared remarkably well in this task, with over half the class able to reconstruct the original sequence with over 77% sequence identity, and with structures whose median ranked in the 91st percentile of all structures of comparable resolution in terms of structure quality. Fourteen percent of the students' structures produced Molprobity steric clash validation scores even better than that of the original structure, suggesting that multiple students achieved an improvement in the overall structure quality compared to the published structure. Students were able to delineate limiting case chemical environments, such as charged interactions or complete solvent exposure, but were less able to distinguish finer details of hydrogen bonding or hydrophobicity. Our results prompt several questions: why were students able to perform so well in their structural validation scores? How were some students able to outperform the 88% sequence identity mark that would constitute a perfect score, given the level of degenerate density or surface residues with poor density? And how can the methodology used by the best students inform the practices of professional X-ray crystallographers?

The authors discuss a creative clinical intervention that derived from collaborative treatment facilitated by art and dance/movement therapist counselors. This interdisciplinary method, called "the button method," expanded into a learning tool in graduate education and professional development trainings. As the method evolved, music therapy was integrated to enhance both the workshop and classroom experiences. The authors describe a five-step model for collaboration using the button method. Examples and considerations are offered as illustrations for clinicians across mental health disciplines interested in exploring collaborative work with creative arts therapists. [ABSTRACT FROM AUTHOR]

Maintaining a healthy protein folding environment is essential for cellular function. Recently, we found that nucleic acids, G-quadruplexes in particular, are potent chaperones for preventing protein aggregation. With the aid of structure-function and NMR analyses of two G-quadruplex forming sequences, PARP-I and LTR-III, we uncovered several contributing factors that affect G-quadruplexes in preventing protein aggregation. Notably, three factors emerged as vital in determining holdase activity of G-quadruplexes: their structural topology, G-quadruplex accessibility and dynamics, and oligomerization state. These factors together appear to largely dictate whether a G-quadruplex is able to prevent partially misfolded proteins from aggregating. Understanding the physical traits that govern the ability of G-quadruplexes to modulate protein aggregation will help elucidate their possible roles in neurodegenerative disease. [ABSTRACT FROM AUTHOR]

Nitric oxide (*NO) generation from conversion of L-arginine to citrulline by nitric oxide synthase isoforms plays a critical role in vascular homeostasis. Loss of *NO is linked to vascular pathophysiology and is decreased in chronically inflamed gut blood vessels in inflammatory bowel disease (IBD; Crohn's disease and ulcerative colitis). Mechanisms underlying decreased .NO production in IBD gut microvessels are not fully characterized. Loss of *NO generation may result from increased arginase (AR) activity, which enzymatically competes with nitric oxide synthase for the common substrate L-arginine. We characterized AR expression in IBD microvessels and endothelial cells and its contribution to decreased *NO production. AR expression was assessed in resected gut tissues and human intestinal microvascular endothelial cells (HIMEC). AR expression significantly increased in both ulcerative colitis and Crohn's disease microvessels and submucosal tissues compared with normal. TNF-[alpha]/lipopolysaccharide increased AR activity, mRNA and protein expression in HIMEC in a time-dependent fashion. RhoA/ ROCK pathway, a negative regulator of *NO generation in endothelial cells, was examined. The RhoA inhibitor C3 exoenzyme and the ROCK inhibitor Y-27632 both attenuated TNF-[alpha]/lipopolysaccharide-induced MAPK activation and blocked AR expression in HIMEC. A significantly higher AR activity and increased RhoA activity were observed in IBD submucosal tissues surrounding microvessels compared with normal control gut tissue. Functionally, inhibition of AR activity decreased leukocyte binding to HIMEC in an adhesion assay. Loss of *NO production in IBD microvessels is linked to enhanced levels of AR in intestinal endothelial cells exposed to chronic inflammation in vivo. endothelium; microvasculature; nitric oxide synthase doi: 10.1152/ajpgi.00499.2006.

The heat shock response maintains cellular homeostasis following sublethal injury. Heat shock proteins (Hsps) are induced by thermal, oxyradical, and inflammatory stress, and they chaperone denatured intracellular proteins. Hsps also chaperone signal transduction proteins, modulating signaling cascades during repeated stress. Gastroesophageal reflux disease (GERD) affects 7% of the US population, and it is linked to prolonged esophageal acid exposure. GERD is characterized by enhanced and selective leukocyte recruitment from esophageal microvasculature, implying activation of microvascular endothelium. We investigated whether phosphatidylinositol 3-kinase (PI3K)/Akt and MAPK regulate Hsp induction in primary cultures of human esophageal microvascular endothelial cells (HEMEC) in response to acid exposure (pH 4.5). Inhibitors of signaling pathways were used to define the contribution of PI3K/Akt and MAPKs in the heat shock response and following acid exposure. Acid significantly enhanced phosphorylation of Akt and MAPKs in HEMEC as well as inducing Hsp27 and Hsp70. The PI3K inhibitor LY-294002, and Akt small interfering RNA inhibited Akt activation and Hsp70 expression in HEMEC. The p38 MAPK inhibitor (SB-203580) and p38 MAPK siRNA blocked Hsp27 and Hsp70 mRNA induction, suggesting a role for MAPKs in the HEMEC heat shock response. Thus acidic pH exposure protects HEMEC through induction of Hsps and activation of MAPK and PI3 kinase pathway. Acidic exposure increased HEMEC expression of VCAM-1 protein, but not ICAM-1, which may contribute to selective leukocyte (i.e., eosinophil) recruitment in esophagitis. Activation of esophageal endothelial cells exposed to acidic refluxate may contribute to GERD in the setting of a disturbed mucosal squamous epithelial barrier (i.e., erosive esophagitis, peptic ulceration). esophagus; esophagitis; gastroesophageal reflux disease; microvasculature; phosphatidylinositol 3-kinase/Akt; VCAM-1

Treatment manuals play an essential role in clinical trials that aim to determine the efficacy of an intervention. Yet, the idea of needing to adhere to a treatment manual may seem counterintuitive to many music therapy clinicians. The purpose of this article is to offer clinician, supervisor, and researcher perspectives on the process of developing and executing a manualized music therapy treatment protocol in a randomized controlled trial. After describing the purpose of treatment manuals in clinical trials, we present the experience of developing a treatment manual through clinician and researcher collaborations. The concept of treatment fidelity and quality assurance monitoring within clinical trials is detailed to provide an inside look at an integral aspect of enacting treatment manuals in efficacy research. We then share reflections from a research clinician and supervisor to demonstrate the opportunities and challenges when working within the guidelines of manualized clinical practice. Providing a reflective perspective on implementation of a manualized treatment protocol allows for a more thorough understanding of the clinical and research processes in the conduct of randomized controlled trials. Collaboration of researchers, clinicians and supervisors is of critical importance for the successful implementation of treatment manuals in clinical trials. [ABSTRACT FROM AUTHOR]