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NASA NTRS2022

Molecular information theory meets protein folding

We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone configurational entropy, secondary structure content, residue burial layers, and mutational studies of protein stability changes. We found that the average information contained in the sequences of evolved proteins is very close to the average information needed to specify a fold ~2.2 ± 0.3 bits/(site operation). The effective alphabet size in evolved proteins equals the effective number of conformations of a residue in the compact unfolded state at around 5. We calculated an energy-to-information conversion efficiency upon folding of around 50%, lower than the theoretical limit of 70%, but much higher than human built macroscopic machines. We propose a simple mapping between molecular information theory and energy landscape theory and explore the connections between sequence evolution, configurational entropy and the energetics of protein folding.

Ignacio E. Sánchez↗

NASA NTRS1992

Growing protein crystals in microgravity - The NASA Microgravity Science and Applications Division (MSAD) Protein Crystal Growth (PCG) program

In collaboration with a medical researcher at the University of Alabama at Birmingham, NASA's Marshall Space Flight Center in Huntsville, Alabama, under the sponsorship of the Microgravity Science and Applications Division (MSAD) at NASA Headquarters, is continuing a series of space experiments in protein crystal growth which could lead to innovative new drugs as well as basic science data on protein molecular structures. From 1985 through 1992, Protein Crystal Growth (PCG) experiments will have been flown on the Space Shuttle a total of 14 times. The first four hand-held experiments were used to test hardware concepts; later flights incorporated these concepts for vapor diffusion protein crystal growth with temperature control. This article provides an overview of the PCG program: its evolution, objectives, and plans for future experiments on NASA's Space Shuttle and Space Station Freedom.

Herren, B.↗

NASA NTRS1989

Protein crystal growth in microgravity

Major advances have been made in several of the experimental aspects of protein crystallography, leaving protein crystallization as one of the few remaining bottlenecks. As a result, it has become important that the science of protein crystal growth is better understood and that improved methods for protein crystallization are developed. Preliminary experiments with both small molecules and proteins indicate that microgravity may beneficially affect crystal growth. For this reason, a series of protein crystal growth experiments using the Space Shuttle was initiated. The preliminary space experiments were used to evolve prototype hardware that will form the basis for a more advanced system that can be used to evaluate effects of gravity on protein crystal growth. Various optical techniques are being utilized to monitor the crystal growth process from the incipient or nucleation stage and throughout the growth phase. The eventual goal of these studies is to develop a system which utilizes optical monitoring for dynamic control of the crystallization process.

Rosenblum, William M.↗

NASA NTRS1988

Protein crystal growth in a microgravity environment

Protein crystal growth is a major experimental problem and is the bottleneck in widespread applications of protein crystallography. Research efforts now being pursued and sponsored by NASA are making fundamental contributions to the understanding of the science of protein crystal growth. Microgravity environments offer the possibility of performing new types of experiments that may produce a better understanding of protein crystal growth processes and may permit growth environments that are more favorable for obtaining high quality protein crystals. A series of protein crystal growth experiments using the space shuttle was initiated. The first phase of these experiments was focused on the development of micro-methods for protein crystal growth by vapor diffusion techniques, using a space version of the hanging drop method. The preliminary space experiments were used to evolve prototype hardware that will form the basis for a more advanced system that can be used to evaluate effects of gravity on protein crystal growth.

Bugg, Charles E.↗

NASA NTRS2002

A microarray immunoassay for simultaneous detection of proteins and bacteria

We report the development and characterization of an antibody microarray biosensor for the rapid detection of both protein and bacterial analytes under flow conditions. Using a noncontact microarray printer, biotinylated capture antibodies were immobilized at discrete locations on the surface of an avidin-coated glass microscope slide. Preservation of capture antibody function during the deposition process was accomplished with the use of a low-salt buffer containing sucrose and bovine serum albumin. The slide was fitted with a six-channel flow module that conducted analyte-containing solutions over the array of capture antibody microspots. Detection of bound analyte was subsequently achieved using fluorescent tracer antibodies. The pattern of fluorescent complexes was interrogated using a scanning confocal microscope equipped with a 635-nm laser. This microarray system was employed to detect protein and bacterial analytes both individually and in samples containing mixtures of analytes. Assays were completed in 15 min, and detection of cholera toxin, staphylococcal enterotoxin B, ricin, and Bacillus globigii was demonstrated at levels as low as 8 ng/mL, 4 ng/mL, 10 ng/mL, and 6.2 x 10(4) cfu/mL, respectively. The assays presented here are very fast, as compared to previously published methods for measuring antibody-antigen interactions using microarrays (minutes versus hours).

Non-NASA Center↗

NASA NTRS1991

Scientific use of Space Station Freedom

The overall strategic science planning of the Office of Space Science and Applications (OSSA) is presented. The science opportunities inherent to the restructured Space Station are discussed and a synopsis of the OSSA implementation plan for Space Station Freedom utilization is offered. Attention is given to the microgravity science and applications facilities, the advanced protein crystal growth facility, the biotechnology facility, the modular combustion facility, and the life sciences facility.

Rhome, Robert C.↗

NASA NTRS1999

Overview of the Microgravity Science Glovebox (MSG)

MSG is a third generation glovebox for Microgravity Science investigations: SpaceLab Glovebox (GBX); Middeck/MIR Gloveboxes (M/MGBX); and GBX and M/MGBX developed by Bradford Engineering (NL). Previous flights have demonstrated utility of glovebox facilities: Contained environment enables broader range of science experiments; Affords better control of video and photographic imaging (a prime data source); Provides better environmental control than cabin atmosphere; and Useful for contingency operations. MSG developed in response to demands for increased work volume, increased capabilities and additional resources. MSG is multi-user facility to support a wide range of small science and technology investigations: Fluid physics; Combustion science; Material science; Biotechnology (cell culturing and protein crystal growth); Space processing; Fundamental physics; and Technology demonstrations. Topics included in this viewgraph are: MSG capabilities; MSG hardware items; MSG, GSE, and OSE items; MSG development approach; and Science utilization.

Wright, Mary Etta↗

NASA NTRS1992

Research objectives, opportunities, and facilities for microgravity science

Microgravity Science in the U.S.A. involves research in fluids science, combustion science, materials science, biotechnology, and fundamental physics. The purpose is to achieve a thorough understanding of the effects of gravitational body forces on physical phenomena relevant to those disciplines. This includes the study of phenomena which are usually overwhelmed by the presence of gravitational body forces and, therefore, chiefly manifested when gravitational forces are weak. In the pragmatic sense, the research involves gravity level as an experimental parameter. Calendar year 1992 is a landmark year for research opportunities in low earth orbit for Microgravity Science. For the first time ever, three Spacelab flights will fly in a single year: IML-1 was launched on January 22; USML-1 was launched on June 25; and, in September, SL-J will be launched. A separate flight involving two cargo bay carriers, USMP-1, will be launched in October. From the beginning of 1993 up to and including the Space Station era (1997), nine flights involving either Spacelab or USMP carriers will be flown. This will be augmented by a number of middeck payloads and get away specials flying on various flights. All of this activity sets the stage for experimentation on Space Station Freedom. Beginning in 1997, experiments in Microgravity Science will be conducted on the Space Station. Facilities for doing experiments in protein crystal growth, solidification, and biotechnology will all be available. These will be joined by middeck-class payloads and the microgravity glove box for conducting additional experiments. In 1998, a new generation protein crystal growth facility and a facility for conducting combustion research will arrive. A fluids science facility and additional capability for conducting research in solidification, as well as an ability to handle small payloads on a quick response basis, will be added in 1999. The year 2000 will see upgrades in the protein crystal growth and fluids science facilities. From the beginning of 1997 to the fall of 1999 (the 'man-tended capability' era), there will be two or three utilization flights per year. Plans call for operations in Microgravity Science during utilization flights and between utilization flights. Experiments conducted during utilization flights will characteristically require crew interaction, short duration, and less sensitivity to perturbations in the acceleration environment. Operations between utilization flights will involve experiments that can be controlled remotely and/or can be automated. Typically, the experiments will require long times and a pristine environment. Beyond the fall of 1999 (the 'permanently-manned capability' era), some payloads will require crew interaction; others will be automated and will make use of telescience.

Bayuzick, Robert J.↗

NASA NTRS1966

Some recent work on prebiological synthesis of organic compounds.

Origin of constituents of nucleic acid and protein molecules, noting biological molecules synthesis under conditions similar to those prevailing in prebiotic Earth, following Oparin-Haldane hypothesis

ABIOGENESIS↗

NASA NTRS2003

Science Issues Associated with the Use of a Microfluidic Chip Designed Specifically for Protein Crystallization

The Iterative Biological Crystallization team in partnership with Caliper Technologies has produced a prototype microfluidic chip for batch crystallization that has been designed and tested. The chip is designed for the mixing and dispensing of up to five solutions with possible variation of the recipe being delivered to two growth wells. Developments that have led to the successful on-chip crystallization of a few model proteins have required investigative insight into many different areas, including fluid mixing dynamics, surface treatments, quantification and fidelity of reagent delivery. This presentation will encompass the ongoing studies and data accumulated toward these efforts.

Holmes, Anna M.↗

NASA NTRS1991

AIAA/IKI Microgravity Science Symposium, 1st, Moscow, USSR, May 13-17, 1991, Proceedings

The state of the art of microgravity science is examined in reviews and reports. Consideration is given to fluid physics; modeling and numerical analysis; crystal growth of electronic materials, proteins, metals, alloys, glasses, and ceramics; biotechnology, combustion science, microgravity hardware, and fundamental phenomena; and education. Particular attention is given to containerless science and technology, a low-gravity two-phase flow with heat transfer, numerical investigation on Benard instability in a finite liquid layer, synthesis and crystallization of refractory compounds from solutions in metallic melts under microgravitation conditions, the long duration protein crystallization experiment aboard the Mir Space Station, directional solidification in immiscible systems, formation of periodic layer structure in oxide melts under different gravity values, opposed flow flame spread in normal, enhanced, and reduced gravity, automatic equipment for semiconductor production in space, and consort and joust sounding rocket missions.

Source record↗

NASA NTRS2003

Biotechnology Protein Expression and Purification Facility

The purpose of the Project Scientist Core Facility is to provide purified proteins, both recombinant and natural, to the Biotechnology Science Team Project Scientists and the NRA-Structural Biology Test Investigators. Having a core facility for this purpose obviates the need for each scientist to develop the necessary expertise and equipment for molecular biology, protein expression, and protein purification. Because of this, they are able to focus their energies as well as their funding on the crystallization and structure determination of their target proteins.

Source record↗

NASA NTRS2006

Efficient Agent-Based Models for Non-Genomic Evolution

Modeling dynamical systems composed of aggregations of primitive proteins is critical to the field of astrobiological science involving early evolutionary structures and the origins of life. Unfortunately traditional non-multi-agent methods either require oversimplified models or are slow to converge to adequate solutions. This paper shows how to address these deficiencies by modeling the protein aggregations through a utility based multi-agent system. In this method each agent controls the properties of a set of proteins assigned to that agent. Some of these properties determine the dynamics of the system, such as the ability for some proteins to join or split other proteins, while additional properties determine the aggregation s fitness as a viable primitive cell. We show that over a wide range of starting conditions, there are mechanisins that allow protein aggregations to achieve high values of overall fitness. In addition through the use of agent-specific utilities that remain aligned with the overall global utility, we are able to reach these conclusions with 50 times fewer learning steps.

Gupta, Nachi↗

NASA NTRS1998

Life and Microgravity Spacelab (LMS)

This document reports the results and analyses presented at the Life and Microgravity Spacelab One Year Science Review meeting. The science conference was held in Montreal, Canada, on August 20-21, 1997, and was hosted by the Canadian Space Agency. The LMS payload flew on the Space Shuttle Columbia (STS-78) from June 20 - July 7, 1996. The LMS investigations were performed in a pressurized Spacelab module and the Shuttle middeck. Forty scientific experiments were performed in fields such as fluid physics, solidification of metals, alloys, and semiconductors, the growth of protein crystals, and animal, human, and plant life sciences. The results demonstrate the range of quality science that can be conducted utilizing orbital laboratories in microgravity.

Downey, James Patton↗

NASA NTRS2001

A novel reagentless sensing system for measuring glucose based on the galactose/glucose-binding protein

The galactose/glucose-binding protein (GBP) is synthesized in the cytoplasm of Escherichia coli in a precursor form and exported into the periplasmic space upon cleavage of a 23-amino-acid leader sequence. GBP binds galactose and glucose in a highly specific manner. The ligand induces a hinge motion in GBP and the resultant protein conformational change constitutes the basis of the sensing system. The mglB gene, which codes for GBP, was isolated from the chromosome of E. coli using the polymerase chain reaction (PCR). Since wild-type GBP lacks cysteines in its structure, introducing this amino acid by site-directed mutagenesis ensures single-label attachment at specific sites with a sulfhydro-specific fluorescent probe. Site-directed mutagenesis by overlap extension PCR was performed to prepare three different mutants to introduce a single cysteine residue at positions 148, 152, and 182. Since these residues are not involved in ligand binding and since they are located at the edge of the binding cleft, they experience a significant change in environment upon binding of galactose or glucose. The sensing system strategy is based on the fluorescence changes of the probe as the protein undergoes a structural change on binding. In this work a reagentless sensing system has been rationally designed that can detect submicromolar concentrations of glucose. The calibration plots have a linear working range of three orders of magnitude. Although the system can sense galactose as well, this epimer is not a potential interfering substance since its concentration in blood is negligible. Copyright 2001 Academic Press.

Non-NASA Center↗

NASA NTRS1991

Electrophoresis experiments in microgravity

The use of the microgravity environment to separate and purify biological cells and proteins has been a major activity since the beginning of the NASA Microgravity Science and Applications program. Purified populations of cells are needed for research, transplantation and analysis of specific cell constituents. Protein purification is a necessary step in research areas such as genetic engineering where the new protein has to be separated from the variety of other proteins synthesized from the microorganism. Sufficient data are available from the results of past electrophoresis experiments in space to show that these experiments were designed with incomplete knowledge of the fluid dynamics of the process including electrohydrodynamics. However, electrophoresis is still an important separation tool in the laboratory and thermal convection does limit its performance. Thus, there is a justification for electrophoresis but the emphasis of future space experiments must be directed toward basic research with model experiments to understand the microgravity environment and fluid analysis to test the basic principles of the process.

Snyder, Robert S.↗

NASA NTRS1998

Second United States Microgravity Laboratory: One Year Report

This document reports the one year science results for the important and highly successful Second United States Microgravity Laboratory (USML-2). The USML-2 mission consisted of a pressurized Spacelab module where the crew performed experiments. The mission also included a Glovebox where the crew performed additional experiments for the investigators. Together, about 36 major scientific experiments were performed, advancing the state of knowledge in fields such as fluid physics, solidification of metals, alloys, and semiconductors, combustion, and the growth of protein crystals. The results demonstrate the range of quality science that can be conducted utilizing orbital laboratories in microgravity and provide a look forward to a highly productive Space Station era.

Vlasse, M.↗

NASA NTRS1998

Second United States Microgravity Laboratory: One Year Report

Vlasse, M↗