Dataset Information

Seven perspectives on GPCR H/D-exchange proteomics methods.

ABSTRACT: Recent research shows surging interest to visualize human G protein-coupled receptor (GPCR) dynamic structures using the bottom-up H/D-exchange (HDX) proteomics technology. This opinion article clarifies critical technical nuances and logical thinking behind the GPCR HDX proteomics method, to help scientists overcome cross-discipline pitfalls, and understand and reproduce the protocol at high quality. The 2010 89% HDX structural coverage of GPCR was achieved with both structural and analytical rigor. This article emphasizes systematically considering membrane protein structure stability and compatibility with chromatography and mass spectrometry (MS) throughout the pipeline, including the effects of metal ions, zero-detergent shock, and freeze-thaws on HDX result rigor. This article proposes to view bottom-up HDX as two steps to guide choices of detergent buffers and chromatography settings: (I) protein HDX labeling in native buffers, and (II) peptide-centric analysis of HDX labels, which applies (a) bottom-up MS/MS to construct peptide matrix and (b) HDX MS to locate and quantify H/D labels. The detergent-low-TCEP digestion method demystified the challenge of HDX-grade GPCR digestion. GPCR HDX proteomics is a structural approach, thus its choice of experimental conditions should let structure lead and digestion follow, not the opposite.

SUBMITTER: Zhang X

PROVIDER: S-EPMC5428523 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Seven perspectives on GPCR H/D-exchange proteomics methods.

Zhang Xi X

F1000Research 20170130

Recent research shows surging interest to visualize human G protein-coupled receptor (GPCR) dynamic structures using the bottom-up H/D-exchange (HDX) proteomics technology. This opinion article clarifies critical technical nuances and logical thinking behind the GPCR HDX proteomics method, to help scientists overcome cross-discipline pitfalls, and understand and reproduce the protocol at high quality. The 2010 89% HDX structural coverage of GPCR was achieved with both structural and analytical r ...[more]

PMID: 28529698

Similar Datasets

Project description:With more classrooms within higher education mobilizing strategies for internationalization, collaborative online international learning (COIL), also referred to as virtual exchange, is an effective approach at offering intercultural competence through experiential learning. This strategy provides students who face barriers to international travel the opportunity to engage with students from other countries in meaningful ways, while enhancing and reinforcing course content. Grounded in the transformative learning theory, this study evaluates the effectiveness of a virtual exchange that was implemented within an undergraduate global public health course. The virtual exchange connected students from the University of Florida (within the US) with medical students in a microbiology course at Ain Shams University in Cairo, Egypt. Using adapted reflection prompts, we assessed the students' knowledge and learning before, during, and after the virtual exchange. This was coupled with a final paper to capture how personal backgrounds and experiences may contribute to their perception of the virtual exchange, as well as if they felt their global perspective had changed or shifted during the experience. Using directed content analysis for each of the measurements, two researchers coded the data independently to then present agreed upon salient themes to the larger group. Of the 28 randomly sampled students who participated in the virtual exchange, seven major themes emerged from the data: Connectedness; Openness; Acquisition of Knowledge and Skills; Communication; Cultural Identity; Anticipation of Options for New Roles, Relationships, and Actions; and Absence of Change. Through this evaluation it was clear there was a variance of different perspectives with many sampled students having diverse lived experiences that influenced their worldview prior to the virtual exchange. Despite course-related barriers, students acknowledged several facilitating factors that improved their intercultural competence and knowledge of course content. The integration of a virtual exchange within the classroom, with careful design and implementation, can provide a unique experience for students and an inclusive approach to learning.

Project description:Collaborative online international learning programs, such as virtual exchange, that utilize telecollaborative activities have been integrated into more classrooms within the higher education setting. These programs provide students exposure to international cultures, perspectives, and ideas is no longer considered "value added", but a prerequisite to entering many workforces. These programmatic objectives compliment Mezirow's Transformative Learning Theory, that substantiates two major elements of transformative learning are critical reflection and dialectical discourse. This study presents the second half of a qualitative inquiry into the prominent themes that arose during a virtual exchange that was conducted in March 2021 between students in the United States (US) enrolled in a global public health course and Egyptian microbiology students. This study sought to expand upon the Transformative Learning Theory through inductive analysis procedures to offer a modernized adaptation of the theoretical framework within international learning environments. Student responses enrolled in an undergraduate global public health course were collected and analyzed by two coders using inductive/open coding to identify salient codes. These codes were then summarized into categories and subsequently defined. Resulting themes include Connectedness, Openness, Acquisition of Knowledge and Skills, Communication, Cultural Identity, Anticipation of Options for New Roles, Relationships, and Actions, and Absence of Change. Several themes have corresponding categories and subcategories. Adult learning environments such as the modern college classroom have changed with the introduction and reliance upon online learning domains, as well as the diversification of higher education student demographics, accentuating the need to inductively analyze student learning processes and outcomes. In doing so, our findings provide a modernized adaptation of the Transformative Learning Theory that allows for adult learning theorists, researchers, and scholars to integrate tenets of transformative learning more appropriately. As such, this provides an opportunity for educators to coalesce the identified mechanisms (e.g., openness, cultural background, anticipation of roles and relationships) to bolster student's willingness and ability to engage in transformative critical reflections. By capitalizing on students' innate characteristics, such as open-mindedness predispositions and cultural background, educators are able to augment transformative learning strategies through tailored assignments and course activities.

Dataset Information

Seven perspectives on GPCR H/D-exchange proteomics methods.

Publications

Seven perspectives on GPCR H/D-exchange proteomics methods.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets