SOLICITATION NOTICE
R -- Computational Analysis of the Membrane Protein BetP using Molecular Simulation and Structural Refinement - Technical Evaluation Criteria - Statement of Work
- Notice Date
- 8/24/2018
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 541715
— Research and Development in the Physical, Engineering, and Life Sciences (except Nanotechnology and Biotechnology)
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Institute on Drug Abuse, 6001 Executive Boulevard, Room 4211, MSC 9559, Bethesda, Maryland, 20892-9559, United States
- ZIP Code
- 20892-9559
- Solicitation Number
- NIHDA201800395
- Archive Date
- 9/19/2018
- Point of Contact
- Stephanie D. Dewitt, Phone: 3014432848
- E-Mail Address
-
stephanie.dewitt@nih.gov
(stephanie.dewitt@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- Statement of Work Technical Evaluation Criteria NON-COMPETITIVE COMBINED SYNOPSIS / SOLICITATION Title: Computational Analysis of the Membrane Protein BetP using Molecular Simulation and Structural Refinement (i)This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued. (ii)The solicitation number is NIHDA201800395 and the solicitation is issued as an request for proposal (RFP). This acquisition is for a commercial item or service and is conducted under the authority of the Federal Acquisition Regulation (FAR) Part 13-Simplified Acquisition Procedures; FAR Subpart 13.5-Simplified Procedures for Certain Commercial Items. THIS IS A NON-COMPETITIVE (NOTICE OF INTENT) COMBINED SYNOPSIS SOLICITATION TO AWARD A CONTRACT OR PURCHASE ORDER WITHOUT PROVIDING FOR FULL OR OPEN COMPETITION (INCLUDING BRAND-NAME). The National Institute on Drug Abuse (NIDA), Station Support Contracts on behalf of the National Institute of Mental Health intends to negotiate and award a purchase order without providing for full and open competition (Including brand-name) to Caroline Koshy, 700 Boulevard E Apt 1D, Weehawken, NJ 07086-6847 for Computational Analysis of the Membrane Protein BetP using Molecular Simulation and Structural Refinement. This acquisition is conducted as non-competitive for a commercial item or service and is conducted under the authority of the FAR Subpart 13.5-Simplified Procedures for Certain Commercial Items and 13.501 Special documentation requirements and the authority of 41 U.S.C. 1901 and the statutory authority of 6.302-1, only one responsible source and no other supplies or services will satisfy agency requirements. (iii)The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-97, dated January 1,2018. (iv)The associated NAICS code 541712 and the small business size standard 1,000 employees. (v) Statement of Need The research program of the Computational Structural Biology Unit, (NINDS/NIH) aims to advance our understanding of the functional mechanisms of membrane proteins related to neuronal transporter proteins, in part through computer-simulation approaches. This research requires a significant, sustained effort to carry out and interrogate the results of molecular simulations for transporters so as to examine the structural dynamics of these molecular systems. Studies over the past 8 years in the Computational Structural Biology Unit have so far resulted in Terabytes of simulation data for BetP in a wide range of conditions that hold within them a wealth of untapped information. The specific aims of this project are: (a) to carry out a systematic analysis of the available molecular simulation data for BetP and thereby to identify common or unusual dynamics of the protein and its interplay with its environment, as well as regions of the protein for which the underlying structural data is ambiguous; (b) to interrogate the underlying structural data in the light of those simulations and carry out refinement of structural models using that data; and finally (c) to utilize the newly-refined structures as starting points for additional molecular simulations, and to carry out additional analysis of those simulations. Novel findings will be written and published as articles in a scientific journal. The aims and deliverables of this project therefore require an individual with world-class experience not only in carrying out and analyzing molecular simulations, but also in the refinement of structural models using X-ray crystallographic and cryo-EM data using the software PHENIX and COOT. In addition, the contractor must have a detailed knowledge of the biological context of the project, namely the properties of BetP and the interplay of its function and regulation with the lipid molecules in its membrane environment, as demonstrated by authorship on published work in the biomedical literature. Background Information The research program of the Computational Structural Biology Unit in the National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), is focused on elucidating the structural mechanisms of biomedically important molecular systems associated with cellular membranes, in part using computationally-intensive, physics-based molecular simulations. Membrane transport proteins are responsible for the uptake of vital nutrients and the extrusion of waste products from cells. Members of this group of proteins are responsible for termination of synaptic transmission by removing neurotransmitters from the synapse. These proteins are the targets of a range of psychoactive compounds including treatments of depression and are implicated in a range of neurological disorders such as Parkinson's disease and addiction. In recent years insights into the detailed molecular mechanisms of these proteins have been garnered mainly through studies of bacterial proteins, which can serve as prototypes due to their similarity with neuronal proteins. One of these bacterial prototypes is the transporter of betaine, BetP, which is crucial for the response of soil bacteria to dry environmental conditions. X-ray crystallographic structures have been determined of BetP that provide snapshots from a molecular movie of its mechanistic cycle. However, much remains to be understood about how these snapshots are interconnected, and how they are controlled by the presence or absence of the betaine molecule. Moreover, BetP has complex regulatory mechanisms involving the ability to function only under certain environmental conditions, such as the presence of specific lipids in the surrounding membrane; so far, little is known about how these features affect the protein and its mechanism. Understanding of these mechanisms is expected to provide important feedback to investigations of neuronal proteins, which depend on their surroundings in similar ways. The simulation method known as Molecular Dynamics (MD) is arguably the most rigorous and promising computational approach to study cellular processes at atomic resolution. The trajectories taken from such MD simulations provide a wealth of complex information that requires advanced training and expertise to interrogate and interpret. The results of these simulations also raise questions about the underlying structural data, inspiring cycles of structural refinement and model rebuilding followed by additional molecular simulations using those refined structures as starting points. See attached Statement of Work for further detail. Technical Evaluation Criteria attached (vi)Period of Performance: One year from date of award. (viii)The following additional contract requirement(s) or terms and conditions as determined by the contracting officer are necessary for this acquisition and consistent with customary commercial practices. FAR 52-213-4-Simplified Acquisitions (Other than Commercial Item) (ix)The Defense Priorities and Allocations System (DPAS) are not applicable to this requirement. Responses to this solicitation must include clear and convincing evidence of the offeror's capability of fulfilling the requirement as it relates to the technical evaluation criteria. In addition the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size must be included in the response. All offerors must have an active registration in the System for Award Management (SAM) www.sam.gov." All responses must be received by 5:00pm EST on Tuesday, September 4th and reference number NIHDA201800395. Responses may be submitted electronically to Stephanie Dewitt, stephanie.dewitt@nih.gov. Fax responses will not be accepted. (x)The name and telephone number of the individual to contact for information regarding the solicitation Stephanie Dewitt, stephanie.dewitt@nih.gov.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NIDA-01/NIHDA201800395/listing.html)
- Place of Performance
- Address: 35 Convent Drive, Building 35A, Room GF 123, Bethesda, Maryland, 20892, United States
- Zip Code: 20892
- Zip Code: 20892
- Record
- SN05056133-W 20180826/180824231704-e662f8ecb9a5f09a1690fc20e2222335 (fbodaily.com)
- Source
-
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