Molecular Biophysics Cluster

This is MCB! Hear from Dr. Engin Serpersu

Serpersu head shot

The Division of Molecular and Cellular Biosciences (MCB) supports fundamental research and related activities designed to promote understanding of complex living systems at the molecular, sub-cellular, and cellular levels. Behind our mission stands a group of individuals whose efforts and great work make this Division outstanding; we are proud to showcase their hard work via this blog.

Dr. Serpersu completed his doctoral degree in biochemistry Hacettepe University Medical School, Ankara, Turkey. He was an Alexander von Humboldt Fellow at Justus Liebig University, Giessen, West Germany, before completing postdoctoral work at Johns Hopkins School of Medicine, Baltimore, MD. He began a teaching career in 1988 at the University of Tennessee in Knoxville, where he rose through the ranks to professor and served a term as chair of the Biochemistry and Cellular and Molecular Biology department. His areas of expertise include biophysical chemistry; protein structure, function, and dynamics; and thermodynamics.

Dr. Serpersu joined MCB in June of 2014 as a rotator (a two-year, temporary program director position) and is now a permanent program director, serving as cluster leader in the Molecular Biophysics cluster. As a program director, he manages proposal reviews and makes funding decisions. As cluster leader, he coordinates activities within the cluster and collaborates with other program directors as well as the broader scientific community to help ensure that awards funded by Molecular Biophysics contribute to NSF’s mission of transforming the frontiers of science and innovating for society. He is also on the CAREER (Faculty Early Career Development) Coordinating Committee and a member of the Oversight Group for National Facilities with the National Institutes of Health.

In his spare time Dr. Serpersu enjoys playing volleyball, attending antique auctions, and walking on the beach.

SPOTLIGHT ON MCB FUNDED SCIENCE

A spotlight illuminates the words 'Spotlight on MCB-funded Science.'

Photo Credit: Matusciac Alexandru/Shutterstock.com

Sharing MCB Science is one of our six blog themes where you can learn about exciting MCB-funded research submitted by our investigators (via this webform). We greatly appreciate the overwhelmingly positive response of the MCB scientific community and have received many more submissions than can be featured in long form on the blog. Enjoy this shorter spotlight of submissions we have received!

a closeup of a cell, it is shapes like a lollypop, a long thin stalk with a rounded top which is darker in color

Joseph K. E. Ortega – Photograph of a stage IV sporangiophore of Phycomyces blakesleeanus with the micro-capillary tip of a pressure probe.

Algal, fungal, and plant cells interact with their environment by regulating their size and shape through expansive growth, an increase in cell volume due predominately to an increase in water uptake. This process presents a special challenge for algae, fungi, and plants because cells in these organisms have an exoskeleton-like cell wall that provides support, protection, and shape.  When water enters these cells, turgor pressure builds up, which stretches (deforms) the cell wall; at the same time, new material is added to the cell wall to fill in the expanded regions and thereby control the size and shape of the enlarging cell. The interconnected processes of water uptake, wall deformation, and control of cell size and shape are crucial for algal, fungal, and plant survival.

Previous research has provided a good description of the molecular and mechanical changes accompanying expansive growth.  Taking advantage of this foundation, Dr. Joseph K. E. Ortega, Professor of Mechanical Engineering at the University of Colorado, Denver, is bringing a new dimension to quantify cellular changes during expansive growth.  He has developed a mathematical model of the interconnected processes, called the Augmented Growth Equations (AGE). As described in his new publication, the model organizes multiple equations to represent the relationships between variables and uses dimensional analysis to produce dimensionless coefficients. The dimensionless coefficients enable researchers to more easily quantify the biophysical processes and better predict how changes in water absorption and cell wall deformation regulate expansive growth. While the model does not address the shape of the cells, the mathematical framework provides insight as to how water uptake and wall deformation are regulated in algal, fungal, and plant cells to control expansive growth during normal conditions and in response to changes in the environment.

This work is partially funded by the Molecular Biophysics Cluster of the Division of Molecular and Cellular Biosciences, Awards #MCB-0948921.

on the left is a still image from an MRI of a chest with the heart and lungs visible. On the right is a graph with the quick heartbead and slower respiration plotted as curves.

Dr. Steven Van Doren – Example of how the TREND software can distinguish the patterns of a heart beating and lungs breathing from an MRI movie

Visual outputs, such as photographs or movies, contain important data from scientific experiments. For example, identifying biologically relevant signals over time (trends) can be challenging, as they may be subtle or mixed into background movements or noise. To identify trends, researchers scour the data looking for specific features, such as peaks, and either mark them by hand, which is time consuming and subjective, or set specific background thresholds in instrumentation, which can result in mistaking signal for noise. In a new publication, Dr. Steven Van Doren, Professor of Biochemistry at the University of Missouri, and his post-doctoral researcher, Dr. Jia Xu, describe a new software program called TREND (Tracking and Resolving Equilibrium and Nonequilibrium population shifts in Data). The software allows researchers to objectively extract information from two-dimensional images or videos, and in another recent publication, they describe extending the analysis to several different types of data.

TREND uses a statistical approach, called principal component analysis (PCA), on a series of individual measurements to compress and organize multivariate data so that researchers can select for and detect changes in a variety of factors over time. The factors can be anything: characteristics of a stream, grades in a class, or gene variants. When applied to movies, such as this sample video of a sunset, a trend in the data, such as the movement of the sun across the sky, can be plotted after removing background noise, such as motion from clouds. Another example is separating the pattern of a heart beating from lungs breathing using TREND (a photo of this video is shown above). TREND is available for licensing and download at http://biochem.missouri.edu/trend and https://nmrbox.org/.

 

This work is partially funded by the Molecular Biophysics Cluster of the Division of Molecular and Cellular Biosciences, Awards #MCB-1409898.

SHARING MCB SCIENCE: UNRAVELING THE DYNAMICS OF TRANSMEMBRANE PROTEINS

Alt Caption (for ADA compliance): Undergraduate honors student Armin Mortazavi, wearing a blue dress shirt, and faculty mentor Dr. Roger Koeppe, wearing a black suitcoat, dress shirt, and glasses, are seated in a laboratory in front of a computer screen looking at deuterium nuclear magnetic resonance data (not shown).

An alpha helix is a stretch of amino acids coiled in three-dimensional space, similar to a spring, which can serve a variety of functions in transmembrane proteins (proteins that span the membrane of a cell). For example, a protein may be anchored into the membrane by one or more alpha helices. Or, since alpha helices physically link the interior and exterior of the cell, they can stimulate the initiation of a signaling cascade inside the cell in response to an external binding event. In addition, multiple alpha helices bundled together can form a channel, enabling ions to move across the hydrophobic interior of the cell membrane where they are otherwise excluded. These are just a small sample of the large number of biological processes and pathways thought to involve alpha helices in transmembrane proteins; therefore, researchers like Dr. Roger Koeppe II and his students are studying alpha helices to fill in the gaps in our fundamental understanding of the dynamics of transmembrane proteins.

One such gap involves identifying the factors that stabilize tilted transmembrane alpha helices. Alpha helices display a variety of orientations within a membrane. Some may reside in the membrane vertical to its axis; others tilt across the membrane at different angles. In his lab in the Department of Chemistry and Biochemistry at the University of Arkansas, Fayetteville, Dr. Koeppe and his students established an experimental model and used a biophysical technique to determine the positions of amino acid residues inside tilted alpha helices in a membrane environment.

In a recent publication, the team described their efforts to design, synthesize, and purify a series of nearly-identical peptides (23 amino acid strands that only varied slightly in amino acid composition). At the ends of each peptide, the team placed deuterium (radioactive isotope) labels on two alanine amino acid residues (at positions 3 and 21). When the team exposed these peptides to lipids (fatty acids that compose the interior of a cell membrane), they formed tilted alpha helices. Using a technique called solid-state deuterium nuclear magnetic resonance (NMR), a series of spectra were gathered for each helix.

As the cover for the March 2016 issue of ChemBioChem depicts, the team detected a deviation between actual and expected orientations of the deuterium-labeled alanine residues at positions 3 and 21 – they actually appeared far from their expected orientations as part of the alpha helix (blue curve). In this way, Dr. Koeppe and his research team discovered that the first and last few amino acids at each end of the tilted alpha helix were unraveled from and no longer part of the alpha helix.

A driving force behind the formation of an alpha helix is the increased stability that results from numerous interactions between the amino acids in the helix, so unraveling these interactions at the ends of the helix may seem to disrupt stability. However, Dr. Koeppe and his team noted that unwinding the helix at both ends creates a larger surface area, enabling new interactions to occur between the amino acids in the helix and the surrounding membrane lipids – providing additional conformational stability in support of the tilt and limiting the helix’s motion. These research findings contribute to our understanding of fundamental biological processes including lipid-protein interactions, membrane protein stability, and membrane biophysics.

When asked about the broader impacts of his research, Dr. Koeppe responded:

“Notably, much of this research involved an undergraduate honors student, Armin Mortazavi. The opportunities for undergraduate students to conduct cutting-edge research alongside graduate students provide students with valuable hands on experience, exposure to new techniques, and mentoring at an early stage in their scientific careers. We have also increased the exposure of communities in Arkansas to science – establishing science cafés and statewide infrastructure projects such as a laboratory where you can explore proteins using virtual reality technology. These efforts broaden the participation of non-traditional or underrepresented groups in science.”

This work is partially funded by the Molecular Biophysics Cluster of the Division of Molecular and Cellular Biosciences, Award #MCB – 1327611.

MOLECULAR BIOPHYSICS INVESTIGATORS AWARDED SOCIETY HONORS

The Division of Molecular and Cellular Biosciences (MCB) congratulates three investigators who recently received distinguished awards in recognition of their contributions to science. Each investigator has been supported in part by MCB’s Molecular Biophysics program.

This is a headshot style photograph of Dr. Gary Pielak in a grey button down shirt with glasses. He is smiling at the camera.Dr. Gary Pielak received the 2016 Carl Brändén Award from the Protein Society. Dr. Pielak is the Kenan Distinguished Professor of Chemistry, Biochemistry, and Biophysics and Vice Chair of Facilities with a joint appointment at the School of Medicine at the University of North Carolina at Chapel Hill. The Carl Brändén Award honors “an outstanding protein scientist who has made exceptional contributions in the areas of education and/or service to the science.”  The service part of the Award reflects, in part, Gary’s stint with us as a MCB Program Director. Dr. Pielak works with his research group to study the equilibrium thermodynamics of proteins under crowded conditions and in living cells using high-resolution in-cell NMR and other methods. His research is supported in part by MCB and NSF’s Division of Chemistry.

Dr. Martin Gruebele was awarded the 2017 Nakanishi Prize by the American Chemical Society. Dr. Gruebele is a 2013 National Academy of Sciences fellow, James R. Eiszner Endowed Chair in Chemistry, Professor of Physics at the Center for Biophysics and Quantitative Biology, and full-time faculty member in the Beckman Institute Nanoelectronics and Nanomaterials group at the University of Illinois at Urbana-Champaign. Much like MCB places high priority on cross-disciplinary research (using computational, physical, mathematical, and engineering tools, technologies, or methodologies to address major biological questions), the Nakanishi prize celebrates “significant work that extends chemical and spectroscopic methods to the study of important biological phenomena.” The Gruebele group uses lasers, microscopy, and computational approaches to explore complex biochemical processes such as transport of unfolded proteins within a cell. This work was supported in part by MCB and NSF’s Division of Chemistry, Division of Materials Research, Division of Undergraduate Education, and the Office of International Science and Engineering.

This is a headshot style photo of Dr. Dave Thirumalai in a grey striped button down shirt. He is smiling at the camera.Dr. Dave Thirumalai received the 2016 Award in Theoretical Chemistry from the Division of Physical Chemistry of the American Chemical Society during the Fall ACS National Meeting in Philadelphia. Dr. Thirumalai is currently Chair of the Department of Chemistry in the College of Natural Sciences at the University of Texas at Austin. As noted on the awards web page, Dr. Thirumalai was recognized for his “outstanding contributions to physical and biophysical chemistry, especially work on protein and RNA folding, protein aggregation, and effects of molecular crowding in cells.” The work of Dr. Thirumalai and his research team when we was at the University of Maryland was supported in part MCB and NSF’s Division of Chemistry, Division of Physics, and the Office of Advanced Cyberinfrastructure.

Please join MCB in congratulating Drs. Pielak, Gruebele, and Thirumalai on their awards!

MCB AT YOUR MEETING: OUTREACH AT THE UNIVERSITY OF PUERTO RICO AT CAROLINA
Image of Dr. Jose Garcia (Investigator at UPRC), Dr. Karilys González Nieves (Investigator at UPRC), Dr. Luis Cubano (Co-Project Director, UPRC Title V), Dr. Reyda González-Nieves (MCB Acting Operations Manager), Dr. Larry Halverson (SSB Program Director), Ms. Raquel Marti (Project Director, UPRC Title V), Dr. Linda Hyman (MCB Division Director), Dr. Wilson Francisco (MB Program Director), Dr. Jose Alvarez (Faculty Development, UPRC Title V), Dr. Moisés Orengo Avilés (UPRC Chancellor), Dr. Awilda Nueñez (Academic Dean at UPRC), and Dr. Jose Santiago (Investigator at UPRC)

Workshop Coordinators and Presenters (from left): Dr. Jose Garcia (Investigator at UPRC), Dr. Karilys González Nieves (Investigator at UPRC), Dr. Luis Cubano (Co-Project Director, UPRC Title V), Dr. Reyda González-Nieves (MCB Acting Operations Manager), Dr. Larry Halverson (SSB Program Director), Ms. Raquel Marti (Project Director, UPRC Title V), Dr. Linda Hyman (MCB Division Director), Dr. Wilson Francisco (MB Program Director), Dr. Jose Alvarez (Faculty Development, UPRC Title V), Dr. Moisés Orengo Avilés (UPRC Chancellor), Dr. Awilda Nueñez (Academic Dean at UPRC), and Dr. Jose Santiago (Investigator at UPRC)

MCB Program Directors and Division leadership regularly attend scientific meetings and workshops to garner input from the scientific community, spread the word about funding opportunities, recruit panelists, and otherwise provide information to encourage the submission of grant proposals. In September, Dr. Linda Hyman (MCB Division Director), Dr. Wilson Francisco (MCB Program Director for Molecular Biophysics (MB)), Dr. Larry Halverson (MCB Program Director for Systems and Synthetic Biology (SSB)), and Dr. Reyda González-Nieves (MCB Acting Operations Manager) traveled to Puerto Rico to support the “How to Write an Excellent Proposal” workshop hosted by the University of Puerto Rico at Carolina (UPRC).

This workshop provided an overview of the National Science Foundation (NSF) and MCB, discussed best practices in NSF grant writing and submission, and highlighted funding opportunities in MCB and across NSF. Prior to the start of the workshop, Drs. Hyman, Francisco, and Halverson met with workshop coordinators at the University of Puerto Rico at Carolina to strategize how best to conduct personalized outreach during the workshop given the larger than expected number of registrants. The workshop was attended by over 60 participants from eight different institutions throughout the island of Puerto Rico. During the morning session of the workshop, MCB representatives gave three presentations: “Overview of NSF and the Directorate for Biological Sciences,” “Cluster Overviews and Opportunities between MCB and other Divisions/Directorates,” and “How to Write an Excellent Proposal.”

Image of MCB Workshop Presenters: (top) Dr. Linda Hyman; (bottom left) Dr. Wilson Francisco; and (bottom right) Dr. Larry Halverson

MCB Workshop Presenters: (top) Dr. Linda Hyman; (bottom left) Dr. Wilson Francisco; and (bottom right) Dr. Larry Halverson

These presentations were followed by individual meetings between MCB representatives and PIs, faculty, and graduate students from the University of Puerto Rico at Carolina to discuss project ideas and their fit for funding opportunities within MCB and NSF. These personalized sessions provided attendees the opportunity to have their questions answered by MCB experts, and to get to know MCB Division Leadership, Program Directors, and staff. In post-workshop feedback, attendees rated their experience “excellent.”

Drs. Hyman, Francisco, Halverson, and González-Nieves felt this workshop was a unique opportunity to encourage new collaborations, cultivate new ideas, discuss funding opportunities, and keep inspiring new and undiscovered talent in the scientific community. The Division of MCB would like to thank the University of Puerto Rico at Carolina for hosting MCB at Your Meeting. To find out about our future travel plans, visit the “MCB at Your Meeting” page on the MCB Blog.

Welcome to MCB Ann Larrow!

Hear from Program Specialist Ann Larrow

What is your educational background?

I have an Associate degree in science lab technology with a concentration in histotechnology; a BA in History; and an MS in Organizational Development and Leadership (a cross-disciplinary degree from Sociology and Political Science). I recently completed coursework for the Project Management Professional certification and have taken a variety of other self-study classes over the years.

What is your position? When did you start working in MCB?

I started as a Program Specialist with MCB on July 11, 2016.

What attracted you to work for NSF?

I was looking for a position where I could continue building a solid resume for professional development. Learning that MCB is interested in creating/maintaining a flexible, adaptable organization by staffing it with creative, forward-looking people was intriguing.

What have you learned so far from your position?

I was impressed with the professionalism of employee orientation; loved hearing HR refer to new hires as “Top Talent,” then following up by inviting us to attract similar talent by updating our Linked In profiles; and have been thrilled with the reception and helpfulness of staff members throughout the building. I have been impressed with what I’ve seen of how the organization uses technology to manage processes and look forward to learning more about where it works best, where it doesn’t work as well, and helping to plan and implement improvements. As for my job duties…ask me in a month or so.

Welcome to MCB Megan Lewis!

Hear from Program Assistant Megan Lewis

What is your educational background?

I recently graduated from Fairfield University’s College of Arts and Sciences with a bachelor’s degree in Biology and a minor in Environmental Studies. Currently, I am attending The George Washington University where I am pursuing a Master’s Degree in Environmental Resource Policy and a Certificate in Geographic Information Systems.

What is your position? When did you start working in MCB?

I am the Program Assistant for the Cellular Dynamics and Function cluster as well as the Molecular Biophysics cluster. I started working with the National Science Foundation in the Directorate for Biological Sciences in December 2015 and moved from the Division of Environmental Biology to the Division of Molecular and Cellular Biosciences in January 2016.

What attracted you to work for NSF?

I had just finished interning with an online public forum that focused on engaging the public in environmental issues, and I was really interested in learning how federal agencies are dealing with these types of problems. With my background in biology, I wanted to find an agency that was working towards solutions to these environmental issues through science rather than strictly policy. The National Science Foundation allows me to learn what scientists across the country are trying to do to better understand these problems and find scientific solutions. In addition, I learn how the federal government decides to fund certain research proposals and what goes into that process.

What have you learned so far from your position?

As I’ve only been at the NSF for a little over two months, I come to work each day and leave learning something new. I never realized how much behind the scenes work there is to manage awards and proposals. Overall, I’d say that the most invaluable thing I’ve learned is that even when we think we have a full understanding of a concept, a principle investigator submits a proposal and opens a new door to a way of thinking about an issue or topic. I was taught in school that science is always evolving and growing, and as a college student I would nod and continue taking notes for a lecture.  But, at the NSF I’ve actually been able to really see the science evolving.

MCB welcomes Dr. Ranajeet Ghose, Program Director for the Molecular Biophysics Cluster.

What were you doing before you came to the NSF?

I am a Professor of Chemistry and Biochemistry at the City College of New York.

What attracted you to work for NSF?

The reason was two-fold: (1) Being a program director allows one to learn about science at the cutting edge beyond ones area of expertise. (2) The NSF has provided me with uninterrupted funding since 2004 starting with a CAREER award. This is an opportunity for me to give back.

What was your first impression of NSF? Has this impression changed since you began serving as a rotator/program director?

My first impression was very positive and it continues to be so. There are some incredibly bright people working here who are quick to realize (and fund) the next big innovation.

What were the personal goals you most wanted to accomplish while at NSF?

Get a broader view of science, in general and molecular biophysics, in particular. This is an opportunity one rarely has in one’s research lab.

What surprised you most about working at NSF?

Nothing really. I have served on multiple panels in the PHY, CHEM and BIO directorates and have been a Committee of Visitors member in the past.

What are some of the challenges of serving as a rotator/program director?

It takes a little while to realize that one is not a panelist when running panels. One has to take great care not to editorialize and let the panelists do their job.

What would you tell someone who is thinking about serving as a program director at NSF?

They should absolutely do it. It would give them an unprecedented opportunity to get a broad view of science than they normally would.

When your friends/colleagues find out that you work at NSF, what do they say or ask?

They worry that my own research may be affected. I tell them that with the Independent Research/Development (IR/D) program and flexible work hours (for an IPA assignee), it allows me to continue my research uninterrupted and supervise my students and postdocs. It actually forces me to organize my time better and perhaps makes me more productive.

Is there anything else you would like to share with the readers?

I would say that this is a great place to work for rotators. The staff and other program directors are fabulous. I expect to leave the NSF a better scientist and a better manager.

This is MCB! Hear from Claudia Garcia

The Division of Molecular and Cellular Biosciences (MCB) supports fundamental research and related activities designed to promote understanding of complex living systems at the molecular, sub-cellular, and cellular levels. Behind our mission stands a group of individuals whose efforts and great work make this Division outstanding; we are proud to showcase their hard work via this blog.

Claudia Garcia has a bachelor’s degree in Information Systems from George Mason University. She is currently working on her second bachelor’s degree in Accounting. She came to NSF through the Pathways Program in February 2013. The Pathways Program in the federal government is designed to provide current students, recent graduates, and students with advanced degrees an opportunity to explore federal careers while enrolled in school. As Program Specialist, Ms. Garcia provides administrative support to the Molecular Biophysics and Cellular Dynamics and Function clusters. Furthermore, Ms. Garcia assists six program directors with the approval proposal cycle, which includes compliance checking, panel set-up, and award distribution. In her spare time, she enjoys traveling and outdoor activities like biking and hiking.