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NASA NTRS2015

Free-Energy Calculations. A Mathematical Perspective

Ion channels are pore-forming assemblies of transmembrane proteins that mediate and regulate ion transport through cell walls. They are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses. They are also essential to cardiac processes, muscle contraction and epithelial transport. Ion channels from lower organisms can act as toxins or antimicrobial agents, and in a number of cases are involved in infectious diseases. Because of their important and diverse biological functions they are frequent targets of drug action. Also, simple natural or synthetic channels find numerous applications in biotechnology. For these reasons, studies of ion channels are at the forefront of biophysics, structural biology and cellular biology. In the last decade, the increased availability of X-ray structures has greatly advanced our understanding of ion channels. However, their mechanism of action remains elusive. This is because, in order to assist controlled ion transport, ion channels are dynamic by nature, but X-ray crystallography captures the channel in a single, sometimes non-native state. To explain how ion channels work, X-ray structures have to be supplemented with dynamic information. In principle, molecular dynamics (MD) simulations can aid in providing this information, as this is precisely what MD has been designed to do. However, MD simulations suffer from their own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. To assess the reliability of MD simulations it is only natural to turn to the main function of channels - conducting ions - and compare calculated ionic conductance with electrophysiological data, mainly single channel recordings, obtained under similar conditions. If this comparison is satisfactory it would greatly increase our confidence that both the structures and our computational methodologies are sufficiently accurate. Channel conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

free energy↗
NASA NTRS1988

High-Resolution Detector For X-Ray Diffraction

Proposed x-ray-sensitive imaging detector offers superior spatial resolution, counting-rate capacity, and dynamic range. Instrument based on laser-stimulated luminescence and reusable x-ray-sensitive film. Detector scans x-ray film line by line. Extracts latent image in film and simultaneously erases film for reuse. Used primarily for protein crystallography. Principle adapted to imaging detectors for electron microscopy and fluorescence spectroscopy and general use in astronomy, engineering, and medicine.

Carter, Daniel C.↗
NASA NTRS1983

Bibliography

A bibliography of articles entered into the data base at the Lunar and Planetary Institute Library from November 1982 through January 1983 is presented. An abstract of each article is given. The subjects covered by the articles include: the motion of the moon and dynamics of the earth-moon system: shape and gravity field of the moon; the physical structure of the moon, its thermal and stress history; the morphology of the lunar surface, the origin and stratigraphy of lunar formations, and mapping of the moon; the chemical composition of the moon, lunar petrology, mineralogy, and crystallography; electromagnetic properties of the moon; the planets; and other objects, including asteroids, comets, meteorites, and cosmic dust.

Kopal, Z.↗
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 NTRS2002

Experimental Replication of Relict "Dusty" Olivine in Type 1B Chondrules

Introduction: Relict "dusty" olivine is considered to be a remnants of previous chondrule forming events based on petrographic and chemical evidence. Dynamic crystallization experiments confirm that dusty olivine can be produced by reduction of FeO-rich olivine in Unequilibrated Ordinary Chondrite (UOC) material. The results of these experiments compliment those of who also produced dusty olivine, but from synthetic starting materials. Techniques: Dynamic crystallization experiments were conducted in which UOC material was reduced in presence of graphite. Starting material was coarsely ground GR095554 or WSG95300 that contained olivine of Fo 65-98. Approximately 75 mg. of UOC material was placed in a graphite crucible and sealed in an evacuated silica tube. The tube was suspended in a gas-mixing furnace operated at 1 log unit below the IW buffer. The experiments were as brief as 1.5 hrs up to 121 hrs. Results: Dusty olivine was produced readily in experiments melted at 1400 C for I hr. and cooled between 5 and 100 C/hr or melted at 1300-1400 C for 24 hours. Fe-rich olivine (dusty olivine precursors) that have been partially reduced were common in the experiments melted at 1400 C and cooled at 1000 C/hr or melted at 1200 C for 24 hrs. Relict olivine is absent in experiments melted at 1400 for 24 hrs, melted above 1400 C, or cooled more slowly than 10 C/hr. Relict olivine in the experiments has minimum Fo value of 83 . Thus even in the shortest experiments the most Fe-rich olivine has been altered significantly. The precursor olivine disappears in a few to many hours depending on temperature. The experiments show Fe-rich olivine in all stages of transition to the new dusty form. The olivine is reduced to form dusty olivine in a matter of a few hours at temperatures less than 1400 C and in minutes at higher temperatures. The reduction appears to proceed from the rim of the crystal inward with time. The reduction appears initially rectilinear as if controlled by crystallography, but with time Fe-metal blebs are randomly distributed throughout the olivine. In a given experiment, dusty olivine can be found in varying stages of development, but in the longest experiments, the Fe-metal blebs are dominant and they appear to be migrating out of the olivine. The composition of the dusty olivine ranges from Fo 94-99. The Cr, Mn, and Ca content of the newly formed, dusty olivine is slightly less on average that the precursor olivine, but is till with the range of type 1 olivine. Chadacrysts in the low Ca pyroxene are most common in the higher temperature, more slowly cooled experiments and range in composition from Fo 90-99. Application to chondrule formation: These experiments place time-temperature limits on the preservation of Fe-rich olivine and the production of dusty olivine during chondrule forming events. The reduction process proceeds in a few hours at temperatures above 1400 C and in 10's of hours at temperature between 1200 and 1300 C. This result further confirms th at chondrules form in a few hours to days as suggested earlier. The experiments also confirm that dusty olivine can form from typical Fe-rich olivine in UOC material during the recycling of such olivine in the chondrule forming process.

Lofgren, Gary E.↗