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Posts Tagged ‘structural biology’

New avenues for research in membrane biology reveals the mobility of protein at work

Curator and Reporter: Dr. Premalata Pati, Ph.D., Postdoc

Membrane proteins (MPs) are proteins that exist in the plasma membrane and conduct a variety of biological functions such as ion transport, substrate transport, and signal transduction. MPs undergo function-related conformational changes on time intervals spanning from nanoseconds to seconds. Many MP structures have been solved thanks to recent developments in structural biology, particularly in single-particle cryo-Electron Microscopy (cryo-EM). Obtaining time-resolved dynamic information on MPs in their membrane surroundings, on the other hand, remains a significant difficulty.

OmpG (Open state) in a fully hydrated dimyristoylphosphatidylcholine (DMPC) bilayer. The protein is shown in light green cartoon. Lipids units are depicted in yellow, while their phosphate and choline groups are illustrated as orange and green van der Waals spheres, respectively. Potassium and chloride counterions are shown in green and purple, respectively. A continuous and semi-transparent cyan representation is used for water.
https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-021-24660-1/MediaObjects/41467_2021_24660_MOESM1_ESM.pdf

Weill Cornell Medicine (WCM) researchers have found that they can record high-speed protein movements while linking them to function. The accomplishment should allow scientists to examine proteins in more depth than ever before, and in theory, it should allow for the development of drugs that work better by hitting their protein targets much more effectively.

The researchers utilized High-Speed Atomic Force Microscopy (HS-AFM) to record the rapid motions of a channel protein and published in a report in Nature Communications on July 16. Such proteins generally create channel or tube-like structures in cell membranes, which open to allow molecules to flow under particular conditions. The researchers were able to record the channel protein’s rapid openings and closings with the same temporal resolution as single channel recordings, a typical technique for recording the intermittent passage of charged molecules through the channel.

Senior author Simon Scheuring, professor of physiology and biophysics in anesthesiology at WCM, said,

There has been a significant need for a tool like this that achieves such a high bandwidth that it can ‘see’ the structural variations of molecules as they work.

Researchers can now produce incredibly detailed photographs of molecules using techniques like X-ray crystallography and electron microscopy, showing their structures down to the atomic scale. The average or dominant structural positionings, or conformations, of the molecules, are depicted in these “images,” which are often calculated from thousands of individual photos. In that way, they’re similar to the long-exposure still photos from the dawn of photography.

Many molecules, on the other hand, are flexible and always-moving machinery rather than fixed structures. Scientists need to generate videos, not still photos, to reveal how such molecules move as they work, to see how their motion translates to function to catch their critical functional conformations, which may only exist for a brief moment. Current techniques for dynamic structural imaging, on the other hand, have several drawbacks, one of which being the requirement for fluorescent tags to be inserted on the molecules being photographed in many cases.

Scheuring and his lab were early adopters of the tag-free HS-AFM approach for studying molecular dynamics. The technology, which can photograph molecules in a liquid solution similar to a genuine cellular environment, employs an extremely sensitive probe, similar to a record player’s stylus, to feel its way over a molecule and therefore build up a picture of its structure. Standard HS-AFM isn’t quick enough to capture the high-speed dynamics of many proteins, but Scheuring and colleagues have developed a modified version, HS-AFM height spectroscopy (HS-AFM-HS), that works much faster by collecting dynamic changes in only one dimension: height.

The researchers used HS-AFM-HS to record the opening and closing of a relatively simple channel protein, OmpG, found in bacteria and widely studied as a model channel protein in the new study, led by the first author Raghavendar Reddy Sanganna Gari, a postdoctoral research associate in Scheuring’s laboratory. They were able to monitor OmpG gating at an effective rate of roughly 20,000 data points per second, seeing how it transitioned from open to closed states or vice versa as the acidity of the surrounding fluid varied.

More significantly, they were able to correlate structural dynamics with functional dynamics in a membrane protein of this size for the first time in a partnership with Crina Nimigean, professor of physiology and biophysics in anesthesiology, and her group at WCM.

The demonstration opens the door for a wider application of this method in basic biology and drug development.

Sanganna Gari stated,

We’re now in an exciting period of HS-AFM technology, for example using this technique to study how some drugs modulate the structural dynamics of the channel proteins they target.

Main Source

Technique reveals proteins moving as they work. By Jim Schnabel in Cornell Chronicle, August 16, 2021.

https://news.cornell.edu/stories/2021/08/technique-reveals-proteins-moving-they-work

Other Related Articles published in this Open Access Online Scientific Journal include the following:

Cryo-EM disclosed how the D614G mutation changes SARS-CoV-2 spike protein structure.

Reporter: Dr. Premalata Pati, Ph.D., Postdoc

https://pharmaceuticalintelligence.com/2021/04/10/cryo-em-disclosed-how-the-d614g-mutation-changes-sars-cov-2-spike-protein-structure/

Proteins, Imaging and Therapeutics

Larry H Bernstein, MD, FCAP, Curator, LPBI

https://pharmaceuticalintelligence.com/2015/10/01/proteins-imaging-and-therapeutics/

From High-Throughput Assay to Systems Biology: New Tools for Drug Discovery

Curator: Stephen J. Williams, PhD

https://pharmaceuticalintelligence.com/2021/07/19/from-high-throughput-assay-to-systems-biology-new-tools-for-drug-discovery/

Imaging break-through: Fusion of microscopy and mass spectrometry produces detailed map of protein distribution

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2015/03/18/imaging-break-through-fusion-of-microscopy-and-mass-spectrometry-produces-detailed-map-of-protein-distribution/

Advanced Microscopic Imaging

Larry H Bernstein, MD, FCAP, Curator, LPBI

https://pharmaceuticalintelligence.com/2016/02/07/advanced-microscopic-imaging/

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The Vibrant Philly Biotech Scene: Focus on Computer-Aided Drug Design and Gfree Bio, LLC

Curator and Interviewer: Stephen J. Williams, Ph.D.

 

 

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This post is the second in a series of posts highlighting interviews with Philadelphia area biotech startup CEO’s and show how a vibrant biotech startup scene is evolving in the city as well as the Delaware Valley area. Philadelphia has been home to some of the nation’s oldest biotechs including Cephalon, Centocor, hundreds of spinouts from a multitude of universities as well as home of the first cloned animal (a frog), the first transgenic mouse, and Nobel laureates in the field of molecular biology and genetics. Although some recent disheartening news about the fall in rankings of Philadelphia as a biotech hub and recent remarks by CEO’s of former area companies has dominated the news, biotech incubators like the University City Science Center and Bucks County Biotechnology Center as well as a reinvigorated investment community (like PCCI and MABA) are bringing Philadelphia back. And although much work is needed to bring the Philadelphia area back to its former glory days (including political will at the state level) there are many bright spots such as the innovative young companies as outlined in these posts.

efavirenz_med-2In today’s post, I had the opportunity to talk with molecular modeler Charles H. Reynolds, Ph.D., founder and CEO of Gfree Bio LLC, a computational structure-based design and modeling company based in the Pennsylvania Biotech Center of Bucks County. Gfree is actually one of a few molecular modeling companies at the Bucks County Biotech Center (I highlighted another company RabD Biotech which structural computational methods to design antibody therapeutics).

Below is the interview with Dr. Reynolds of Gfree Bio LLC and Leaders in Pharmaceutical Business Intelligence (LPBI):

LPBI: Could you briefly explain, for non-molecular modelers, your business and the advantages you offer over other molecular modeling programs (either academic programs or other biotech companies)? As big pharma outsources more are you finding that your company is filling a needed niche market?

GfreeBio: Gfree develops and deploys innovative computational solutions to accelerate drug discovery. We can offer academic labs a proven partner for developing SBIR/STTR proposals that include a computational or structure-based design component. This can be very helpful in developing a successful proposal. We also provide the same modeling and structure-based design input for small biotechs that do not have these capabilities internally. Working with Gfree is much more cost-effective than trying to develop these capabilities internally. We have helped several small biotechs in the Philadelphia region assess their modeling needs and apply computational tools to advance their discovery programs. (see publication and collaboration list here).

LPBI: Could you offer more information on the nature of your 2014 STTR award?

GfreeBio: Gfree has been involved in three successful SBIR/STTR awards in 2014.   I am the PI for an STTR with Professor Burgess of Texas A&M that is focused on new computational and synthetic approaches to designing inhibitors for protein-protein interactions. Gfree is also collaborating with the Wistar Institute and Phelix Therapeutics on two other Phase II proposals in the areas of oncology and infectious disease.

LPBI: Why did you choose the Bucks County Pennsylvania Biotechnology Center?

GfreeBio: I chose to locate my company at the Biotech Center because it is a regional hub for small biotech companies and it provides a range of shared resources that are very useful to the company. Many of my most valuable collaborations have resulted from contacts at the center.

LPBI: The Blumberg Institute and Natural Products Discovery Institute has acquired a massive phytochemical library. How does this resource benefit the present and future plans for GfreeBio?

GfreeBio: To date Gfree Bio has not been an active collaborator with the Natural Products Insititute, but I have a good relationship with the Director and that could change at any time.

LPBI: Was the state of Pennsylvania and local industry groups support GfreeBio’s move into the Doylestown incubator? Has the partnership with Ben Franklin Partners and the Center provided you with investment and partnership opportunities?

GfreeBio: Gfree Bio has not been actively seeking outside investors, at least to date. We have been focused on growing the company through collaborations and consulting relationships. However, we have benefitted from being part of the Keystone Innovation Zone, a state program that provides incentives for small technology-based businesses in Pennsylvania.

LPBI: You will be speaking at a conference in the UK on reinventing the drug discovery process through tighter collaborations between biotech, academia, and non-profit organizations.  How do you feel the Philadelphia area can increase this type of collaboration to enhance not only the goals and missions of nonprofits, invigorate the Pennsylvania biotech industry, but add much needed funding to the local academic organizations?

GfreeBio: I think this type of collaboration across sectors appears to be one of the most important emerging models for drug discovery.   The Philadelphia region has been in many ways hard hit by the shift of drug discovery from large vertically integrated pharmaceutical companies to smaller biotechs, since this area was at the very center of “Big Pharma.” But I think the region is bouncing back as it shifts more to being a center for biotech. The three ingredients for success in the new pharma model are great universities, a sizeable talent pool, and access to capital. The last item may be the biggest challenge locally. The KIZ program (Keystone Innovation Zone) is a good start, but the region and state could do more to help promote innovation and company creation. Some other states are being much more aggressive.

LPBI: In addition, the Pennsylvania Biotechnology Center in Bucks County appears to have this ecosystem: nonprofit organizations, biotechs, and academic researchers. Does this diversity of researchers/companies under one roof foster the type of collaboration needed, as will be discussed at the UK conference? Do you feel collaborations which are in close physical proximity are more effective and productive than a “virtual-style” (online) collaboration model? Could you comment on some of the collaborations GfreeBio is doing with other area biotechs and academics?

GfreeBio: I do think the “ecosystem” at the Pennsylvania Biotechnology Center is important in fostering new innovative companies. It promotes collaborations that might not happen otherwise, and I think close proximity is always a big plus. As I mentioned before, many of the current efforts of Gfree have come from contacts at the center.   This includes SBIR/STTR collaborations and contract work for local small biotech companies.

LPBI: Thompson Reuters just reported that China’s IQ (Innovation Quotient) has risen dramatically with the greatest patents for pharmaceuticals and compounds from natural products. Have you or your colleagues noticed more competition or business from Chinese pharmaceutical companies?

GfreeBio: The rise of Asia, particularly China, has been one of the most significant recent trends in the pharmaceutical industry. Initially, this was almost exclusively in the CRO space, but now China is aggressively building a fully integrated domestic pharmaceutical industry.

LPBI: How can the Philadelphia ecosystem work closer together to support greater innovation?

GfreeBio: A lot has happened in recent years to promote innovation and company creation in the region. There could always be more opportunities for networking and collaboration within the Philadelphia community. Of course the biggest obstacle in this business is often financing. Philadelphia needs more public and private sources for investment in startups.

LPBI: Thank you Dr. Reynolds.

Please look for future posts in this series on the Philly Biotech Scene on this site

Also, if you would like your Philadelphia biotech startup to be highlighted in this series please contact me: sjwilliamspa@comcast.net or @StephenJWillia2.
Our site is read by ~ 570,000 readers, among them thousand international readers daily and followed by thousands of Twitter followers.

 

Other posts on this site in this VIBRANT PHILLY BIOTECH SCENE SERIES OR referring to PHILADELPHIA BIOTECH include:

RAbD Biotech Presents at 1st Pitch Life Sciences-Philadelphia

The Vibrant Philly Biotech Scene: Focus on Vaccines and Philimmune, LLC

What VCs Think about Your Pitch? Panel Summary of 1st Pitch Life Science Philly

1st Pitch Life Science- Philadelphia- What VCs Really Think of your Pitch

LytPhage Presents at 1st Pitch Life Sciences-Philadelphia

Hastke Inc. Presents at 1st Pitch Life Sciences-Philadelphia

PCCI’s 7th Annual Roundtable “Crowdfunding for Life Sciences: A Bridge Over Troubled Waters?” May 12 2014 Embassy Suites Hotel, Chesterbrook PA 6:00-9:30 PM

Pfizer Cambridge Collaborative Innovation Events: ‘The Role of Innovation Districts in Metropolitan Areas to Drive the Global an | Basecamp Business

Mapping the Universe of Pharmaceutical Business Intelligence: The Model developed by LPBI and the Model of Best Practices LLC

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