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Structural Dynamics of Viral Proteins: Development and Application of Multiscale Computational Methods for Studying Viral Capsids, Proteins and Membrane Systems

Award Number: R35GM119762
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 07/15/2016
PERIOD OF PERFORMANCE END DATE: 02/28/2027

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Structural Dynamics of Viral Proteins: Development and Application of Multiscale Computational Methods for Studying Viral Capsids, Proteins and Membrane Systems - This proposal presents a vision for my research program over the next five years. My lab is engaged in the application and development of multiscale computational methods to study biomolecular systems, with main driver interests in non-enveloped virus capsids, biomembranes and protein dynamics. Through these studies we will provide modeling tools, gain insights into the regulation and mechanisms of biomolecular functions and apply deep learning methods to gain a new comprehension of protein communication and conformational changes. The main motivation in our viral capsid studies is to understand the determinants and molecular mechanisms of infection processes leading to capsid uncoating/disassembly. Our work on virus systems will expand into the genus of Enteroviruses, which include severe health threats such as poliovirus, EV-A71 and EV-D68. There are numerous high resolution structures of mature, uncoating intermediates and genome released states of enteroviruses which enable this research direction. Significant findings from these studies will include detailed structural and energetic information regarding viral infection related processes, which will be valuable in the development of anti-viral therapies against these agents. Our interests in biomembranes are centrally related to how bilayer lipid composition and shape affect the structure, dynamics and functional properties of lipids, peptides and proteins. Our work on virus capsids and biomembranes will involve multi-resolution approaches including atomistically resolved and coarse-grained models. For virus capsids, coarse-grained models will be advanced to study uncoating and genome release and software will be developed and distributed for this purpose. Our work on biomembranes will be supported by the continued development and enhancement of our BUMPy software for constructing curved membrane systems with biologically inspired shapes. We will also study protein components of the innate immune system, where we will employ supervised machine learning approaches to perform classification of simulations from different structural or biochemical states. Using these approaches will allow us to define new collective variables to compute pathways and energetics of molecular recognition and activation. For all the proposed studies we will employ advanced multiscale modeling methods and have existing or identified new experimental collaborators with mutual interest in these systems and questions, to partner with in these investigations.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $398,475 )
2025	2025	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	001	9	3/24/2025	NON-COMPETING CONTINUATION	$398,475
2025	2024	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	000	8	11/8/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $398,475

Issue Date FY: 2024 ( Subtotal = $442,750 )
2024	2024	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	000	8	2/29/2024	NON-COMPETING CONTINUATION	$398,475
2024	2024	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	001	8	6/19/2024	NON-COMPETING CONTINUATION	$44,275
														Subtotal = $442,750

Issue Date FY: 2023 ( Subtotal = $442,750 )
2023	2023	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	000	7	3/14/2023	NON-COMPETING CONTINUATION	$442,750
														Subtotal = $442,750

Issue Date FY: 2022 ( Subtotal = $442,750 )
2022	2022	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	001	6	2/25/2022	COMPETING CONTINUATION	$442,750
2022	2022	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	003	6	8/29/2022	COMPETING CONTINUATION	$118,789
2022	2020	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	000	5	2/16/2022	NON-COMPETING CONTINUATION	$0
2022	2020	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	002	5	8/29/2022	NON-COMPETING CONTINUATION	-$118,789
														Subtotal = $442,750

Issue Date FY: 2020 ( Subtotal = $385,900 )
2020	2020	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	000	5	5/18/2020	NON-COMPETING CONTINUATION	$385,900
														Subtotal = $385,900

Issue Date FY: 2019 ( Subtotal = $386,415 )
2019	2019	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	000	4	5/20/2019	NON-COMPETING CONTINUATION	$386,415
														Subtotal = $386,415

Issue Date FY: 2018 ( Subtotal = $463,941 )
2018	2018	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	001	3	8/31/2018	SUPPLEMENT FOR EXPANSION	$77,040
2018	2018	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	000	3	5/24/2018	NON-COMPETING CONTINUATION	$386,901
														Subtotal = $463,941

Issue Date FY: 2017 ( Subtotal = $387,360 )
2017	2017	UNIVERSITY OF CONNECTICUT	438 WHITNEY RD EXTENSION UNIT 1133	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	000	2	6/1/2017	NON-COMPETING CONTINUATION	$387,360
														Subtotal = $387,360

Issue Date FY: 2016 ( Subtotal = $240,595 )
2016	2016	UNIVERSITY OF CONNECTICUT	438 WHITNEY ROAD EXTENSION	STORRS	CT	06269	CAPITOL	USA	Biomedical Research and Research Training	000	1	7/15/2016	NEW	$240,595
														Subtotal = $240,595

Grand Total All Awards = $3,590,936

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Structural Dynamics of Viral Proteins: Development and Application of Multiscale Computational Methods for Studying Viral Capsids, Proteins and Membrane Systems

Award Number: R35GM119762

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 07/15/2016

PERIOD OF PERFORMANCE END DATE: 02/28/2027

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