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Rigidity and flexibility of large bio-molecular assemblies

Award Number: R01GM109456
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: 09/01/2013
PERIOD OF PERFORMANCE END DATE: 04/30/2020

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Rigidity and flexibility of large bio-molecular assemblies - DESCRIPTION (provided by applicant): Biological macromolecules (such as proteins) are flexible structures held together by a variety of stabilizing interactions. The aim of this proposa is to advance our understanding of how the three-dimensional structure and dynamics of large molecular assemblies relate to their biological functions. We propose a systematic (mathematical, algorithmic and biological) study of rigidity-based methods for simulating slow-motion conformational changes in biomolecules. Decomposing large molecules into rigid clusters leads to structures with a much smaller number of degrees of freedom. We treat them as kinematic linkages, i.e. as collections of articulated rigid bodies interconnected through various types of flexible joints. We will develop new methods for motion simulation, based on these kinematic abstractions. The essence of this approach is a substantial dimensionality reduction of the conformational space. To test and experiment with our ideas, we will develop new software for generating kinematically-realistic motions of biological macromolecules, built upon and integrated into the recently released software infrastructure KINARI (http://kinari.cs.umass.edu) developed in PI Streinu's group. We will evaluate and benchmark our models and our new methods, for accuracy and speed, against other coarse-grained models (such as Normal Mode Analysis) and will validate them on biological data. The mathematical and computational approach is to develop a rigorous deformation theory for molecular structures modeled as systems of articulated bodies, observant of the topology of their underlying configuration spaces and leading to effective simulation techniques through motions that are guided by essential kinematic constraints. This research is anticipated to enhance the general understanding of flexibility and allostery in proteins, to impact protocols for protein structure determination using low-resolution experimental data and, ultimately, to inform the rational design of new drugs based on improved understanding of protein functions as they relate to flexibility and motion.


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: 2020 ( Subtotal = $0 )
2020	2017	TRUSTEES OF THE SMITH COLLEGE, THE	1 CHAPIN WAY	NORTHAMPTON	MA	01063	HAMPSHIRE	USA	Biomedical Research and Research Training	000	5	9/30/2020	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2019 ( Subtotal = $0 )
2019	2017	TRUSTEES OF THE SMITH COLLEGE, THE	1 CHAPIN WAY	NORTHAMPTON	MA	01063	HAMPSHIRE	USA	Biomedical Research and Research Training	000	5	4/29/2019	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2017 ( Subtotal = $286,445 )
2017	2017	TRUSTEES OF THE SMITH COLLEGE, THE	1 CHAPIN WAY	NORTHAMPTON	MA	01063	HAMPSHIRE	USA	Biomedical Research and Research Training	003	5	4/18/2017	NON-COMPETING CONTINUATION	$257,800
2017	2017	TRUSTEES OF THE SMITH COLLEGE, THE	1 CHAPIN WAY	NORTHAMPTON	MA	01063	HAMPSHIRE	USA	Biomedical Research and Research Training	004	5	6/5/2017	NON-COMPETING CONTINUATION	$28,645
2017	2016	TRUSTEES OF THE SMITH COLLEGE, THE	1 CHAPIN WAY	NORTHAMPTON	MA	01063	HAMPSHIRE	USA	Biomedical Research and Research Training	002	4	1/23/2017	EXTENSION WITH OR WITHOUT FUNDS	$424,742
2017	2015	TRUSTEES OF THE SMITH COLLEGE, THE	1 CHAPIN WAY	NORTHAMPTON	MA	01063	HAMPSHIRE	USA	Biomedical Research and Research Training	001	3	1/23/2017	NON-COMPETING CONTINUATION	-$286,505
2017	2014	TRUSTEES OF THE SMITH COLLEGE, THE	1 CHAPIN WAY	NORTHAMPTON	MA	01063	HAMPSHIRE	USA	Biomedical Research and Research Training	000	2	1/23/2017	NON-COMPETING CONTINUATION	-$138,237
														Subtotal = $286,445

Issue Date FY: 2016 ( Subtotal = $286,445 )
2016	2016	SMITH COLLEGE	7 College Lane	NORTHAMPTON	MA	01060	HAMPSHIRE	USA	Biomedical Research and Research Training	000	4	4/30/2016	EXTENSION WITH OR WITHOUT FUNDS	$286,445
														Subtotal = $286,445

Issue Date FY: 2015 ( Subtotal = $286,505 )
2015	2015	SMITH COLLEGE	7 College Lane	NORTHAMPTON	MA	01060	HAMPSHIRE	USA	Biomedical Research and Research Training	000	3	4/20/2015	NON-COMPETING CONTINUATION	$286,505
														Subtotal = $286,505

Issue Date FY: 2014 ( Subtotal = $286,505 )
2014	2014	SMITH COLLEGE	7 College Lane	NORTHAMPTON	MA	01060	HAMPSHIRE	USA	Biomedical Research and Research Training	000	2	4/21/2014	NON-COMPETING CONTINUATION	$286,505
														Subtotal = $286,505

Issue Date FY: 2013 ( Subtotal = $286,505 )
2013	2013	SMITH COLLEGE	7 College Lane	NORTHAMPTON	MA	01060	HAMPSHIRE	USA	Biomedical Research and Research Training	000	1	8/28/2013	NEW	$286,505
														Subtotal = $286,505

Grand Total All Awards = $1,432,405

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Rigidity and flexibility of large bio-molecular assemblies

Award Number: R01GM109456

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: 09/01/2013

PERIOD OF PERFORMANCE END DATE: 04/30/2020

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