Sunday, December 22, 2024 12/22/2024

Large-scale simulations of ribosomal decoding

Award Number: R01GM072686
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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Multi-drug resistant bacteria present an increasing problem in US hospitals. To design new antibiotics that are effective against these bacteria, it is important to understand drug-target interactions and the targets themselves. We will study a major antibiotic target: the ribosome. Many ribosome antibiotics interfere with the process of decoding by the ribosome ("tRNA selection"). The rate-limiting step of decoding is accommodation, where the tRNA moves from a partially bound state (A/T state) to its fully bound position (A/A state) inside the ribosome. Structural biology techniques have determined the structure of the ribosome before and after accommodation. Kinetic experiments have determined accommodation rates. It is difficult, however, to study the process of accommodation in atomic detail experimentally and the detailed effects of antibiotics. While molecular dynamics simulations have been used to characterize spontaneous transitions in smaller protein complexes, the large size and complexity of the ribosome have made similar studies of the ribosome computationally prohibitive. In our preliminary data, we have combined the high performance computing resources at Los Alamos National Laboratory with all-atom reduced-model potentials to study accommodation of tRNA into the ribosome. Here, we will use large- scale molecular simulation to study key features of accommodation and the effects of antibiotics. We will closely integrate molecular dynamics with single molecule studies to form a more coherent picture of ribosome decoding.


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: 2024 ( Subtotal = $330,388 )
2024	2024	TRIAD NATIONAL SECURITY LLC	335 CENTRAL PARK SQ	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	001	19	6/17/2024	NON-COMPETING CONTINUATION	$33,039
2024	2024	TRIAD NATIONAL SECURITY LLC	335 CENTRAL PARK SQ	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	19	12/8/2023	NON-COMPETING CONTINUATION	$297,349
														Subtotal = $330,388

Issue Date FY: 2023 ( Subtotal = $332,842 )
2023	2023	TRIAD NATIONAL SECURITY LLC	335 CENTRAL PARK SQ	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	18	12/22/2022	NON-COMPETING CONTINUATION	$299,557
2023	2023	TRIAD NATIONAL SECURITY LLC	335 CENTRAL PARK SQ	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	001	18	2/15/2023	NON-COMPETING CONTINUATION	$33,285
														Subtotal = $332,842

Issue Date FY: 2022 ( Subtotal = $336,629 )
2022	2022	TRIAD NATIONAL SECURITY, LLC	335 CENTRAL PARK SQUARE, TA-00, BUILDING 767, MS A187	LOS ALAMOS	NM	87545	LOS ALAMOS	USA	Biomedical Research and Research Training	000	17	12/14/2021	NON-COMPETING CONTINUATION	$302,963
2022	2022	TRIAD NATIONAL SECURITY, LLC	335 CENTRAL PARK SQUARE TA-00 BUILDING 767 MS A187	LOS ALAMOS	NM	87545	LOS ALAMOS	USA	Biomedical Research and Research Training	001	17	6/27/2022	NON-COMPETING CONTINUATION	$33,666
														Subtotal = $336,629

Issue Date FY: 2021 ( Subtotal = $340,346 )
2021	2021	TRIAD NATIONAL SECURITY, LLC	335 CENTRAL PARK SQUARE, TA-00, BUILDING 767, MS A187	LOS ALAMOS	NM	87545	LOS ALAMOS	USA	Biomedical Research and Research Training	001	16	1/28/2021	COMPETING CONTINUATION	$340,346
2021	2021	TRIAD NATIONAL SECURITY, LLC	335 CENTRAL PARK SQUARE TA-00 BUILDING 767 MS A187	LOS ALAMOS	NM	87545	LOS ALAMOS	USA	Biomedical Research and Research Training	003	16	7/11/2021	COMPETING CONTINUATION	$9,449
2021	2018	LOS ALAMOS NATIONAL SECURITY, LLC	335 CENTRAL PARK SQ	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	15	1/18/2021	NON-COMPETING CONTINUATION	$0
2021	2018	LOS ALAMOS NATIONAL SECURITY, LLC	335 CENTRAL PARK SQ	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	002	15	7/11/2021	NON-COMPETING CONTINUATION	-$9,449
														Subtotal = $340,346

Issue Date FY: 2020 ( Subtotal = $0 )
2020	2018	LOS ALAMOS NATIONAL SECURITY, LLC	335 CENTRAL PARK SQ	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	15	7/29/2020	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2018 ( Subtotal = $337,999 )
2018	2018	LOS ALAMOS NATIONAL SECURITY, LLC	BIKINI ATOLL RD SM 30	LOS ALAMOS	NM	87545	LOS ALAMOS	USA	Biomedical Research and Research Training	000	15	6/25/2018	NON-COMPETING CONTINUATION	$337,999
														Subtotal = $337,999

Issue Date FY: 2017 ( Subtotal = $337,447 )
2017	2017	LOS ALAMOS NATIONAL SECURITY, LLC	BIKINI ATOLL RD SM 30	LOS ALAMOS	NM	87545	LOS ALAMOS	USA	Biomedical Research and Research Training	000	14	6/30/2017	NON-COMPETING CONTINUATION	$337,447
														Subtotal = $337,447

Issue Date FY: 2016 ( Subtotal = $336,892 )
2016	2016	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	13	8/24/2016	NON-COMPETING CONTINUATION	$336,892
														Subtotal = $336,892

Issue Date FY: 2015 ( Subtotal = $336,489 )
2015	2015	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	001	12	8/28/2015	COMPETING CONTINUATION	$336,489
2015	2014	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	11	8/25/2015	NON-COMPETING CONTINUATION	$0
														Subtotal = $336,489

Issue Date FY: 2014 ( Subtotal = $315,167 )
2014	2014	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	11	7/1/2014	NON-COMPETING CONTINUATION	$315,167
														Subtotal = $315,167

Issue Date FY: 2013 ( Subtotal = $304,136 )
2013	2013	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	10	7/17/2013	NON-COMPETING CONTINUATION	$304,136
														Subtotal = $304,136

Issue Date FY: 2012 ( Subtotal = $315,167 )
2012	2012	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	9	7/30/2012	NON-COMPETING CONTINUATION	$315,167
														Subtotal = $315,167

Issue Date FY: 2011 ( Subtotal = $315,166 )
2011	2011	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	8	7/29/2011	COMPETING CONTINUATION	$315,166
2011	2010	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	001	7	7/29/2011	NON-COMPETING CONTINUATION	$0
														Subtotal = $315,166

Issue Date FY: 2010 ( Subtotal = $274,899 )
2010	2010	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	7	6/28/2010	NON-COMPETING CONTINUATION	$274,899
														Subtotal = $274,899

Issue Date FY: 2009 ( Subtotal = $261,867 )
2009	2009	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	6	6/22/2009	NON-COMPETING CONTINUATION	$261,867
														Subtotal = $261,867

Issue Date FY: 2008 ( Subtotal = $260,652 )
2008	2008	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	5	6/27/2008	NON-COMPETING CONTINUATION	$260,652
														Subtotal = $260,652

Issue Date FY: 2007 ( Subtotal = $260,033 )
2007	2007	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	4	8/2/2007	NON-COMPETING CONTINUATION	$260,033
														Subtotal = $260,033

Issue Date FY: 2006 ( Subtotal = $266,995 )
2006	2006	LOS ALAMOS NATIONAL SECURITY LLC	4200 WEST JEMEZ ROAD	LOS ALAMOS	NM	87544	LOS ALAMOS	USA	Biomedical Research and Research Training	000	3	9/20/2006	NON-COMPETING CONTINUATION	$266,995
														Subtotal = $266,995

Issue Date FY: 2005 ( Subtotal = $285,110 )
2005	2005	UNIVERSITY OF CALIFORNIA, LOS ALAMOS NAT'L LABORATORY	POST OFFICE BOX 1663	LOS ALAMOS	NM	87545	LOS ALAMOS	USA	Biomedical Research and Research Training	000	1	6/27/2005	NEW	$285,110
														Subtotal = $285,110

Grand Total All Awards = $5,548,224

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Large-scale simulations of ribosomal decoding

Award Number: R01GM072686

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

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