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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 NTRS1999

Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study

Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations for 161.5 ns. Initially placed in the aqueous phase as a beta-strand, the peptide rapidly adsorbs to the interface, where it adopts an amphipathic conformation. The marginal presence of nonamphipathic structures throughout the complete trajectory indicates that the corresponding conformations are strongly disfavored at the interface. It is further suggestive that folding in an interfacial environment proceeds through a pathway of successive amphipathic intermediates. The energetic and entropic penalties involved in the conformational changes along this pathway markedly increase the folding time scales of LQQLLQQLLQL, explaining why the alpha-helix, the hypothesized lowest free energy structure for a sequence with a hydrophobic periodicity of 3.6, has not been reached yet. The formation of a type I beta-turn at the end of the simulation confirms the importance of such motifs as initiation sites allowing the peptide to coalesce towards a secondary structure. Proteins 1999;36:383-399. Copyright 1999 Wiley-Liss, Inc.

NASA Center ARC↗

NASA NTRS1972

Large scale wind tunnel investigation of a folding tilt rotor

A twenty-five foot diameter folding tilt rotor was tested in a large scale wind tunnel to determine its aerodynamic characteristics in unfolded, partially folded, and fully folded configurations. During the tests, the rotor completed over forty start/stop sequences. After completing the sequences in a stepwise manner, smooth start/stop transitions were made in approximately two seconds. Wind tunnel speeds up through one hundred and seventy-five knots were used, at which point the rotor mast angle was increased to four degrees, corresponding to a maneuver condition of one and one-half g.

Source record↗

NASA NTRS1974

Digital controller for a Baum folding machine

A digital controller for controlling the operation of a folding machine enables automatic folding of a desired number of sheets responsive to entry of that number into a selector. The controller includes three decade counter stages for corresponding rows of units, tens and hundreds push buttons. Each stage including a decimal-to-BCD encoder, a buffer register, and a digital or binary counter. The BCD representation of the selected count for each digit is loaded into the respective decade down counters. Pulses generated by a sensor and associated circuitry are used to decrease the count in the decade counters. When the content of the decade counter reaches either 0 or 1, a solenoid control valve is actuated which interrupts operation of the machine. A repeat switch, when actuated, prevents clearing of the buffer registers so that multiple groups of the same number of sheets can be folded without reentering the number into the selector.

Bryant, W. H.↗

NASA NTRS1975

Tectonic analysis of folds in the Colorado plateau of Arizona

Structural mapping and analysis of folds in Phanerozoic rocks in northern Arizona, using LANDSAT-1 imagery, yielded information for a tectonic model useful in identifying regional fracture zones within the Colorado Plateau tectonic province. Since the monoclines within the province developed as a response to differential movements of basement blocks along high-angle faults, the monoclinal fold pattern records the position and trend of many elements of the regional fracture system. The Plateau is divided into a mosaic of complex, polyhedral crustal blocks whose steeply dipping faces correspond to major fracture zones. Zones of convergence and changes in the trend of the monoclinal traces reveal the corners of the blocks. Igneous (and salt) diapirs have been emplaced into many of the designated zones of crustal weakness. As loci of major fracturing, folding, and probably facies changes, the fractures exert control on the entrapment of oil and gas.

Davis, G. H.↗

NASA NTRS1982

Protein folding, protein structure and the origin of life: Theoretical methods and solutions of dynamical problems

Theoretical methods and solutions of the dynamics of protein folding, protein aggregation, protein structure, and the origin of life are discussed. The elements of a dynamic model representing the initial stages of protein folding are presented. The calculation and experimental determination of the model parameters are discussed. The use of computer simulation for modeling protein folding is considered.

Weaver, D. L.↗

NASA NTRS1985

The Presidents' Day cyclone of 18-19 February 1979 - Influence of upstream trough amplification and associated tropopause folding on rapid cyclogenesis

The Presidents' Day cyclone of 18-19 February, 1979 is analyzed based on conventional radiosonde data, infrared and visible satellite imagery, water vapor images and ozone measurement. The well-known synoptic-scale characteristics of the PJ-trough system are described, and evidence for the development of the tropopause fold are presented. Processes contributing to the formation of the fold are discussed in terms of an evaluation of the Sawyer-Eliassen circulation equation and a diagnostic evaluation of the ageostrophic winds and vertical motion near the polar jet streak. The documentation of stratospheric extrusions and their possible role in cyclogenesis is reviewed, and Eulerian and Lagrangian diagnostics are used to establish a connection between the tropopause fold associated with the polar jet streak and rapid cyclogenesis along the East Coast. Conservation of potential vorticity expressed in isentropic coordinates is used as a constraint from which to view cyclogenesis.

Uccellini, L. W.↗

NASA NTRS1985

Structural Mapping of Folded Sedimentary Environments from Satellite Images: an Example from Central Asia

In the Tadjik Depression, in Soviet Central Asia, in the absence of existing geologic or topographic maps, an enhanced LANDSAT multispectral scanner image was used in combination with field data to produce a 1:250000 geologic map of the Vakhsh fold-and-thrust belt and adjacent autochthon. Several structural conclusions are reached as a result of this mapping. Deformation of the Cretaceous and Tertiary strata of the fold-and-thrust belt is, in the central Tadjik Depression, conspicuously absent north of a buried basement fault that marks the hinge-zone of the Late Mesozoic passive margin. But, in the eastern half of the depression, thrusting has moved coherent sheets northward, over the block fault, these sheets now lie flat atop the autochthon to the north. The crustal structure inherited from the Mesozoic extensional phase has strongly influenced the Late Cenozoic pattern of deformation, producing the fold-and-thrust belt that is markedly asymmetric. The development of the thrust system has included the progressive overlapping of thrust: the later thrusts apparently formed internal to the older thrusts, and subsequently overrode them.

Leith, W.↗

NASA NTRS1987

Tropopause fold structure determined from airborne lidar and in situ measurements

Airborne differential absorption lidar and in situ data obtained during the April 20, 1984 flight experiment conducted over Nevada and California are analyzed. The O3 and aerosols profiles and in situ measurements reveal a 2.0-km-deep layer (with high O3 concentrations and enhanced aerosol backscattering) and a correlation of 0.8 between O3 and aerosol backscatter (with both values decreasing about 25 percent along the central axis of the fold). It is observed that the cold boundary of the fold has weaker gradients, larger-scale undulations, and more irregularity than the warm boundary. The potential vorticity distribution along the flight path was derived from radiosonde data. A positive correlation between the O3 mixing ratio and the potential vorticity values in the fold is detected; the average ratio between O3 and potential vorticity is 50.2 ppbv/10 to the -5th sq cm deg per g s.

Browell, E. V.↗

NASA NTRS1991

Faulting and folding in the formation of planetary wrinkle ridges

Topographic profiles for planetary wrinkle ridges compiled from high-resolution Lunar Topographic Orthophoto maps for the moon and from monoscopic photoclinometry data for Mars reveal that many of these ridges are characterized by an elevation offset between one side of a ridge and the other. To investigate the relative importance of faulting and folding in the formation of planetary wrinkle ridges, this paper develops a model of subsurface structure, based on observations and measurements of surface physiography and topography by Golombek and Franklin (1987) and Plescia (1990), and assumptions of subsurface structure, which makes it possible to estimate shortening across wrinkle ridges on Moon and Mars. According to this model, total ridge shortening is on the order of 100 m; shortening due to faulting exceeds shortening due to folding for fault dips up to 60-80 deg, implying that faults beneath many wrinkle ridges break the surface to accomodate the greater displacement along the fault than is accomodated in the fold.

Golombek, M. P.↗

NASA NTRS1993

Multiple-fold clustered processor mesh array

The multiple-fold clustered processor mesh array is a triangular organization of clustered processing elements. This multiple-fold array maintains functional equivalence to the nearest neighbor mesh computer with uni-directional interprocessor communications, but with half the number of connection wires. In addition, the connectivity of the multiple-folded organization is superior to the standard square mesh due to the improved connectivity between the clustered processors. One of the primary application areas targeted is High Performance Architectures for image processing.

Pechanek, Gerald G.↗

NASA NTRS1994

Formation of fold and thrust belts on Venus due to horizontal shortening of a laterally heterogeneous lithosphere

An outstanding question relevant to understanding the tectonics of Venus is the mechanism of formation of fold and thrust belts, such as the mountain belts that surround Lakshmi Planum in western Ishtar Terra. These structures are typically long (hundreds of km) and narrow (many tens of km), and are often located at the margins of relatively high (km-scale) topographic rises. Previous studies have attempted to explain fold and thrust belts in various areas of Venus in the context of viscous and brittle wedge theory. However, while wedge theory can explain the change in elevation from the rise to the adjacent lowland, it fails to account for a fundamental aspect of the deformation, i.e., the topographic high at the edge of the rise. In this study we quantitatively explore the hypothesis that fold and thrust belt morphology on Venus can alternatively be explained by horizontal shortening of a lithosphere that is laterally heterogeneous, due either to a change in thickness of the lithosphere or the crust. Lateral heterogeneities in lithosphere structure may arise in response to thermal thinning or extensive faulting, while variations in crustal thickness may arise due to either spatially variable melting of mantle material or by horizontal shortening of the crust. In a variable thickness lithosphere or crust that is horizontally shortened, deformation will tend to localize in the vicinity of thickness heterogeneity, resulting in a higher component of dynamic topography there as compared to elsewhere in the shortening lithosphere. This mechanism may thus provide a simple explanation for the topographic high at the edge of the rise.

Zuber, M. T.↗

NASA NTRS1999

Early Events in the Folding of an Amphipathic Peptide A Multi- Nanosecond Molecular Dynamics Study

Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations over 161.5 nanoseconds. Initially placed in the aqueous phase as a beta-strand, the peptide rapidly adsorbs to the interface, where it adopts an amphipathic conformation. The marginal presence of non-amphipathic structures throughout the complete trajectory indicate- that the corresponding conformations are strongly disfavored at the interface. It is further suggestive that folding in an interfacial environment proceeds through a pathway of successive amphipathic intermediates. The energetic and entropic penalties involved in the conformational changes along this pathway markedly increase the folding time-scales of LQQLLQQLLQL, explaining why the alpha-helix, the hypothesized lowest free energy structure for a sequence with a hydrophobic periodicity of 3.6, has not been reached yet. The formation of a type I beta-turn at the end of the simulation confirms the importance of such motifs as initiation sites allowing the peptide to coalesce towards a secondary structure.

Chipot, Christophe↗

NASA NTRS1997

Peptide Folding and Translocation Across the Water-Membrane Interface

The ability of small peptides to organize at aqueous interfaces was examined by performing a series of large-scale, molecular dynamics computer simulations of several peptides composed of two amino acids, nonpolar leucine (L) and polar glutamine (Q). The peptides differed in size and sequence of the amino acids. Studies on dipeptides LL, LQ, QL and QQ were extended to two heptamers, LQQLLQL and LQLQLQL, designed to maximize interfacial stability of an alpha-helix and a beta-strand, respectively, by exposing polar side chains to water and nonpolar side chains to a nonpolar phase. Finally, a transition of an undecamer, composed entirely of leucine residues, from a disordered structure in water to an alpha-helix in a nonpolar phase representing the interior of the membrane was investigated. Complete folding of a peptide in solution was accomplished for the first time in computer simulations. The simulations revealed several basic principles governing the sequence-dependent organization of peptides at interfaces. Short peptides tend to accumulate at interfaces and acquire ordered structures, providing that they have a proper sequence of polar and nonpolar amino acids. The dominant factor determining the interfacial structure of peptides is the hydrophobic effect, which is manifested at aqueous interfaces as a tendency for polar and nonpolar groups of the solute to segregate into the aqueous and nonpolar phases, respectively. If peptides consist of nonpolar residue's only, they become inserted into the nonpolar phase. As demonstrated by the example of the leucine undecamer, such peptides fold into an alpha-helix as they partition into the nonpolar medium. The folding proceeds through an intermediate, called 3-10-helix, which remains in equilibrium with the alpha-helix. Once in the nonpolar environment, the peptides can readily change their orientation with respect to the interface from parallel to perpendicular, especially in response to local electric fields. The ability of nonpolar peptides to modify both the structure and orientation with respect to the interface from parallel to perpendicular, especially in response to local electric fields. The ability of nonpolar peptides to modify both the structure and orientation with changing external conditions may have provided a simple mechanism of transmitting signals from the environment to the interior of a cell.

Pohorille, Andrew↗

NASA NTRS2004

The X-38 V-201 Fin Fold Actuation Mechanism

The X-38 Vehicle 201 (V-201) is a space flight prototype lifting body vehicle that was designed to launch to orbit in the Space Shuttle orbiter payload bay. Although the project was cancelled in May 2003, many of the systems were nearly complete. This paper will describe the fin folding actuation mechanism flight subsystems and development units as well as lessons learned in the design, assembly, development testing, and qualification testing. The two vertical tail fins must be stowed (folded inboard) to allow the orbiter payload bay doors to close. The fin folding actuation mechanism is a remotely or extravehicular activity (EVA) actuated single fault tolerant system consisting of seven subsystems capable of repeatedly deploying or stowing the fins.

Lupo, Christian↗

NASA NTRS1999

Patients' choice of portable folding chairs to reduce symptoms of orthostatic hypotension

Patients with neurogenic orthostatic hypotension may use portable folding chairs to prevent or reduce symptoms of low blood pressure. However, a concomitant movement disorder may limit the use of these chairs in daily living. In this prospective study, 13 patients with orthostatic hypotension, balance disturbance associated with motor disability, or both examined three commercially available portable folding chairs. A questionnaire was used to document the characteristics in chair design that were relevant for satisfactory use to these patients. Armrests, seat width, and an adjustable sitting height were found to be important features of a portable folding chair. One chair was selected by 11 of 13 patients to fit most needs.

NASA Discipline Cardiopulmonary↗

NASA NTRS2005

Conservation of Fold and Topology of Functional Elements in Thiamin Pyrophosphate Enzymes

Thiamin pyrophosphate (TPP)-dependent enzymes are a highly divergent family of proteins binding both TPP and metal ions. They perform decarboxylation-hydroxyaldehydes. Prior -ketoacids and of a common - (O=)C-C(OH)- fragment of to knowledge of three-dimensional structures of these enzmes, the GDGY25-30NN sequence was used to identify these enzymes. Subsequently, a number of structural studies on those enzymes revealed multi-subunit organization and the features of the two duplicate cofactor binding sites. Analyzing the structures of 44 structurally known enzymes, we found that the common structure of these enzymes is reduced to 180-220 amino acid long fragments of two PP and two PYR domains that form the [PP:PYR]2 binding center of two cofactor molecules. The structures of PP and PYR are arranged in a similar fold-sheet with triplets of helices on both sides.Dconsisting of a six-stranded Residues surrounding the cofactors are not strictly conserved, but they provide the same interatomic contacts required for the catalytic functions that these enzymes perform while maintaining interactive structural integrity. These structural and functional amino acids are topological counterparts located in the same positions of the conserved fold of sets of PP and PYR domains. Additional parallels include short fragments of sequences that link these amino acids to the fold and function. This report on the structural commonalities amongst TPP dependent enzymes is thought to contribute new approaches to annotation that may assist in advancing the functional proteomics of TPP dependent enzymes, and trace their complexity within evolutionary context.

Dominiak, P.↗

NASA NTRS2017

A Method for Designing Conforming Folding Propellers

As the aviation vehicle design environment expands due to the in flux of new technologies, new methods of conceptual design and modeling are required in order to meet the customer's needs. In the case of distributed electric propulsion (DEP), the use of high-lift propellers upstream of the wing leading edge augments lift at low speeds enabling smaller wings with sufficient takeoff and landing performance. During cruise, however, these devices would normally contribute significant drag if left in a fixed or windmilling arrangement. Therefore, a design that stows the propeller blades is desirable. In this paper, we present a method for designing folding-blade configurations that conform to the nacelle surface when stowed. These folded designs maintain performance nearly identical to their straight, non-folding blade counterparts.

Litherland, Brandon L.↗