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Wedekind Lab Co-Crystal Structure of HIV RNA in complex with a Lab-Evolved Protein on the Cover of Nucleic Acids Research

Tuesday, July 31, 2018

Nucleic Acid Cover

Co-crystal structure of HIV trans-activation response (TAR) RNA (rainbow ribbon) in complex with lab-evolved protein, TBP6.7 (blue Cα ribbon). A short peptide (pink) binds TAR outside the context of TBP6.7. (art by Joseph Wedekind). The underlying electron micrograph shows HIV virions (CDC image #13472 by Maureen Metcalfe and Tom Hodge).

Nucleic Acids Research Breakthrough article describes structure of HIV TAR complex with engineered binding protein and structure-based synthesis of antagonist

Investigators at multiple research institutes, led by Dr. Joseph Wedekind (University of Rochester) have described the high resolution crystal structure of a laboratory-evolved protein bound to its tightly associated HIV TAR RNA target, and subsequent synthesis and characterization of a stapled peptide mimic of the predominant RNA binding epitope in that protein. The study provided a detailed framework for peptide-mediated TAR recognition that might be generally applicable to target other disease-relevant RNAs.

HIV/AIDS is a global health threat that requires new insights into viral targets, especially those that resist mutation and promote novel aspects of the viral life cycle. In these respects, the HIV-1 trans-activation response (TAR) RNA is of ongoing interest. Previously, investigators (including some from this author group) developed methods to produce a unique lab-evolved protein (‘TBP6.7’) that recognizes TAR with extraordinarily high affinity compared to known TAR binders [Crawford et al. McNaughton (2016) ACS Chem. Biol. 8, 2206]. However, the molecular determinants of TAR recognition remained obscure, thus limiting the investigators’ ability to further exploit that discovery. The crystal structure of this complex allowed investigators to determine that only a subset of the ‘evolved’ protein sequences are actually involved in RNA binding, with the preponderance of interactions localized to a short β-hairpin. This observation led them to synthesize a short, stapled peptide that mimics the β-hairpin and attenuates TAR-dependent transcription in HeLa nuclear lysate.

The study reported here [Belashov et al. Wedekind (2018) Nucleic Acids Res. 46, 6401-6415] is highly multi-disciplinary, spanning crystallography, site-directed mutagenesis, calorimetry, cell-surface display, ELISA, transcription assays, molecular dynamics simulations, and constrained peptide synthesis. In the end, the conversion of the parental RNA binding protein from single- to double-stranded RNA recognition implies that the protein has sufficient plasticity to recognize numerous RNA folds.

Reviewers and editors familiar with the work have stated that the study is “a strong contribution to a difficult field” that “will have substantial impact in the field of RNA recognition, ranging from applied (specifically targeting therapeutically relevant RNAs) to basic (understanding how RRMs bind to specific RNAs in the cell)”

The Wedekind laboratory at the University of Rochester investigates the mechanisms of action of non-protein-coding (nc)RNAs, and is interested especially in the three-dimensional architectures of these RNAs and how they bind to specific small molecules or peptides, leading to conformations that alter biological function. The research was supported by the University of Rochester Center for AIDS Research, and the National Institutes of Health.

Biochemistry & Biophysics Students Going Places

Tuesday, June 12, 2018

By Dr. Joseph Wedekind

The Department of Biochemistry & Biophysics is pleased to announce the winners of the Sayeeda Zain Fall Travel awards: Debapratim Dutta, Sierra Fox and Hong Zhu.

The Sayeeda Zain Travel Award honors the distinguished career and charitable life of Dr. Sayeeda Zain. The award is given in recognition of research excellence to support travel and related expenses associated with attendance at a scientific conference or corporate internship to gain practical experience.

Debapratim (Dave) Dutta is presenting a poster and was invited to give a talk at the Annual RNA Society Meeting (Berkeley, CA). Sierra Fox presented a poster and was a Keystone Symposia Future of Science Fund Scholarship recipient at the Keystone Symposia in Chromatin Architecture and Chromatin Organization, and Gene Control in Development and Disease Symposia (Whistler, BC, Canada). Hong Zhu presented a poster at the III International Conference on Vaccines Research and Development (Washington, DC).

Debapratim (Dave) Dutta

Debapratim (Dave) Dutta

Sierra Fox

Sierra Fox

Hong Zhu

Hong Zhu

Wishing our graduates well at the 2018 Commencement Dinner

Wednesday, May 23, 2018

The 2018 Ph.D.Commencement Dinner was held at the Daisy Flour Mill. Following introductions from Edith Lord, Senior Associate Dean for Graduate Education and Jennifer Stripay, representing the University of Rochester Alumni Council, Awards were presented to three graduating PhD students:

Vincent du Vigneaud Award: Anthony DiPiazza, Microbiology and Immunology, “Insights into CD4 T Cell-Mediated Immunity to Influenza Viruses.” The award is conferred by the Office of Graduate Education to a graduating student whose thesis is judged superior and unique in potential for stimulating and extending research in the field.

Wallace O. Fenn Award: Benjamin Plog, Pathology, “Novel Insight into Regulation of Glymphatic Flow with Implications for Traumatic Brain Injury.” The award is given annually to a graduating student judged to have performed especially meritorious research and who presented a Ph.D. thesis suitable to honor the name of Wallace Fenn, former professor and chair of physiology.

Marvel-Dare F. Nutting Award (recognizing an outstanding Biochemistry PhD): Amber Cutter, whose PhD dissertation was on “Molecular Characterization of Nucleosome Recognition by Linker Histone H1.0.” 

Commencement Dinner Photos

2018 Commencement Dinner

Congratulations to the 2018 Biochemistry Graduates!

Tuesday, May 22, 2018

students at commencement

Pictured are Anne Cheng, Venice Magunga, and Anmol Almast following the Arts, Sciences & Engineering commencement ceremony Sunday. Photo reproduced from 5-21-18 issue of @Rochester

The Department of Biochemistry and Biophysics congratulates the 20 young men and women who received their B.S. in Biochemistry this weekend. We look forward to their continued success in their future training and careers! In addition to the University-wide celebration, these graduates received their diplomas at a ceremony in The Class of ’62 Auditorium, attended by their families, friends, and faculty from the many departments involved in their training. The ceremony was officiated by Beth Grayhack, Ph.D., Director of the Undergraduate Program (Biochemistry and Biophysics), and was enriched by addresses from Sina Ghaemmaghami, Ph.D. (Biology) and Mark Dumont (Biochemistry and Biophysics).

Biochemistry and Biophysics Holds Annual Department Awards Ceremony

Sunday, May 20, 2018

On Friday May, 18th the department held it's annual awards ceremony in the Neuman Room. At the event this year the following awards were awarded to our current B&B graduate students:

  • Bloor Award - Christina Brule and Lu Han
  • Metzger Award - Karl J. P. Smith
  • Sherman Award – Bronwyn Lucas
  • Neuman Award – Chapin Cavender
  • Grossfield Award – Sreyoshi Sur (talk), Lauren Benoodt (poster)
  • Student Seminar Award – Fall: Bronwyn Lucas (BMB), Leslie Salas-Estrada (BSCB)
    Spring: Viktoriya Anokhina (BMB), Daniel Steiner (BSCB)
  • Hooker Award – Dudarshika DeZoysa (BMB), Christina Lai (BMB)
  • Goodman Fellowship (3rd place for the Messersmith Award) – Leslie Salas-Estrada
  • Faculty Award – Mark Dumont (BMB), Alan Grossfield (BSCB)
  • Zain Award – Christine Lai, Lingfeng Luo, Louis Smith

Congratulations to all the winners and our 2018 graduates!

View photos from the event.

A Hidden Promise in the Language Cells Use to Communicate

Tuesday, May 8, 2018

Scientists have begun to implicate extracellular vesicles and exosomes in everything from cancer to viral infections to basic neural functioning. To Lynne Maquat, the J. Lowell Orbison Distinguished Service Alumni Professor in the Department of Biochemistry and Biophysics, the process shows how parts of the genome we used to think of as junk actually have important functions. “You could say that the host domesticated a viral sequence for its own purposes,” Maquat says. “That’s the beauty of our complexity—[these elements] allow tinkering or fine-tuning of genes.”

Read More: A Hidden Promise in the Language Cells Use to Communicate

Latest Rochester Medicine Explores the 'Spirit and Science' of Lynne Maquat

Tuesday, May 1, 2018

maquat

The magazine's new issue, now in an interactive, flip-book format, highlights the investigative work of the J. Lowell Orbison Endowed Chair, as well as the impressive efforts of our medical students, alumni and faculty—past and present.

Read More: Latest Rochester Medicine Explores the 'Spirit and Science' of Lynne Maquat

Maquat Wins the 2018 FASEB Excellence in Science Award

Sunday, April 22, 2018

Lynne Maquat, PhD, received the 2018 Federation of American Societies for Experimental Biology (FASEB) Excellence in Science Award during the Experimental Biology 2018 meeting in San Diego, hosted by the American Society for Biochemistry and Molecular Biology (ASBMB). The award recognizes women whose outstanding career achievements in biological science have contributed significantly to the understanding of a particular discipline through scientific achievements, training of students and postdoctoral fellows, and contributions to the broader scientific community. Maquat is best known for unraveling RNA’s role in sickness and in health and for advocating for young women in the sciences. View Dr. Maquat’s award interview on ASBMB’s interviews page.

Read more: Maquat celebrated for her service and scientific achievements
Read more: Unraveling RNA and Stereotypes: Q&A with award-Winning Scientist Lynne Maquat

Looking to RNA for Answers

Friday, March 23, 2018

Cancer is a group of diseases in which the body’s cells divide uncontrollably and invade nearby tissues. Scientists at Wilmot Cancer Institute and the University of Rochester’s Center for RNA Biology are working to understand more about how and why this happens.

One piece of the puzzle they’re studying is ribonucleic acid, or RNA, which is found in all cells. RNA is made in the nucleus of a cell from our DNA, which holds the instruction manual for life. RNA puts those instructions into action.

RNA comes in many forms. One form, called messenger RNA (mRNA), carries those instructions out of the nucleus to the ribosomes, where proteins are made. These proteins are essential for functions ranging from digestion to protecting us from disease. If the mRNA has a bad copy of instructions, then either a faulty protein or no protein is created, leading to diseases like cancer.

Understanding the quality-control system

Lynne E. Maquat, Ph.D., director of the Center for RNA Biology, studies a quality control process that blocks cells from making faulty proteins. Called nonsense-mediated mRNA decay (NMD), this process comes into play when mRNA has a set of instructions with a mistake that will lead to short or incomplete proteins. NMD acts like a set of factory inspectors that find and destroy this mRNA before the faulty proteins can be made.

Sometimes, though, NMD doesn’t catch the mistakes and harmful proteins are made. This process plays a part in one-third of all inherited diseases, such as cystic fibrosis and muscular dystrophy, and one-third of all acquired diseases, including a number of cancers.

One reason is that tumors can influence how these inspectors work. Maquat and her team are looking for ways to stop tumors from interfering with NMD with the goal of finding new ways to treat cancer.

Slowing cancer’s growth

A team from Maquat’s lab has also identified a protein called Tudor-SN that is important as cells prepare to divide. This protein controls many microRNAs, molecules that are very small RNAs that control the expression of tens of thousands of genes.

The scientists found that when Tudor-SN is removed from human cells, levels of hundreds of microRNAs go up, putting the brakes on genes that encourage cell growth. This slows down the process of cell division known as the cell cycle, which goes awry in cancer.

Maquat and Reyad A. Elbarbary, Ph.D., a former post-doctoral fellow in Maquat’s lab, have filed a patent application for methods that target Tudor-SN for the treatment and prevention of cancer. They continue to study how Tudor-SN works in concert with other molecules and proteins so that scientists can identify the most appropriate drugs to target it.

Other avenues

Scientists at the Center for RNA Biology are also looking at RNA’s other roles in cancer to find new treatment strategies. For example, Mitchell O’Connell, Ph.D., is studying how microRNAs can interfere with the way genes are expressed and lead to cancer. He and his team are using the gene-editing technology known as CRISPR, which he has adapted to edit RNA, to learn more about the proteins involved in this process.

Yi-Tao Yu, Ph.D., and his team are studying various ways to modify mRNA so that it can override mistakes in genetic instructions. Sometimes there’s a premature stop signal that orders a cell to stop reading the genetic instructions in mRNA partway through the process, resulting in an incomplete protein. The Yu lab is working to alter mRNA in ways that turn “stop” signals into “go” signals, creating full length proteins and preventing diseases like cancer. 

The study of RNA biology is allowing scientists and physicians to explore entirely new treatment strategies for cancer and a wide range of other genetic and acquired disorders.

Learn more about the work being done at the Center for RNA Biology.

By Lydia Fernandez

Read More: Looking to RNA for Answers

Maquat Wins 17th Annual Wiley Prize in Biomedical Sciences

Tuesday, February 20, 2018

The Wiley Foundation today announced the 17th annual Wiley Prize in Biomedical Sciences will be awarded to Lynne E. Maquat for elucidating the mechanism of nonsense-mediated messenger RNA decay, a fundamental process whereby cells remove defective transcripts that can encode toxic proteins.

Dr. Maquat is a Professor at the Department of Biochemistry & Biophysics in the School of Medicine and Dentistry, the Founding Director of the Center for RNA Biology: From Genome to Therapeutics, the Founding Chair of the University of Rochester Graduate Women in Science, and the J. Lowell Orbison Endowed Chair at the University of Rochester in Rochester, New York.

“The 2018 Wiley Prize honors Dr. Maquat, whose work illuminated how our cells prevent production of toxic proteins by removing defective messenger RNAs," said Dr. Titia de Lange, chairperson of the awards jury for the Wiley Prize at the Rockefeller University in New York City.

“The Wiley Foundation honors research that champions novel approaches and challenges accepted thinking in the biomedical sciences. The work of the 2018 Wiley Prize recipient Lynne Maquat truly upholds this mission,” said Deborah Wiley, Chair of the Wiley Foundation. “We are pleased to highlight the impact that her research on messenger RNA decay pathways has had in advancing our knowledge of the cellular cause of many human diseases.”

Read More: Maquat Wins 17th Annual Wiley Prize in Biomedical Sciences

New Issue of Opportunities to Explore - February 12-16, 2018

Friday, February 9, 2018

This week there is a workshop on Navigating a career fair/expo, the PDA monthly meeting, a career expo on river campus and workshops from Future Faculty, CIRTL and GWIS. The week ends with a PONS luncheon and a Thinkers and Drinkers meeting

Looking further ahead, Stephen Tajc provides a look at his career in URBEST's series. Workshops on job descriptions and handling difficult conversations are available and CIRTL provides several events throughout the month. All this and more in the latest issue of OTE!

Latest Issue of Opportunities to Explore - February 12-16, 2018

Dutta, Fox, and Zhu Win Sayeeda Zain Travel Award

Tuesday, January 2, 2018

The department is pleased to announce the winners of the Sayeeda Zain Fall Travel awards: Debapratim Dutta, Sierra Fox and Hong Zhu.

The Sayeeda Zain Travel Award honors the distinguished career and charitable life of Dr. Sayeeda Zain. The award is given in recognition of research excellence to support travel and related expenses associated with attendance at a scientific conference or corporate internship to gain practical experience. The next round of Sayeeda Zain Travel Awards will be offered in Spring 2018.

Thank you to all those who applied and congratulations to Dave, Sierra and Hong!