Physicochemical Biology: Conquered Boundaries and New Horizons

In this paper, we shall consider the main evolutionary stages that occurred within the field of physicochemical biology during the 20th century, following the determination of the tertiary structure of DNA by Watson and Crick and the subsequent successes in the X-ray structural analysis of biopolymers. The authors ideas on the pre-emptive problems and the methods used in physicochemical biology in the 21st century are also presented, including an investigation of the dynamics of biochemical processes, studies of the functions of unstructured proteins, as well as single-molecule investigations of enzymatic processes and of biopolymer tertiary structure formation.

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Physicochemical Biology: Conquered Boundaries and New Horizons

Acta Naturae ◽

10.32607/actanaturae.10624 ◽

2012 ◽

Vol 4 (2) ◽

pp. 36-43

Author(s):

D. G. Knorre

Keyword(s):

Structural Analysis ◽

21St Century ◽

Single Molecule ◽

Tertiary Structure ◽

X Ray ◽

Biochemical Processes ◽

New Horizons ◽

Physicochemical Biology ◽

Unstructured Proteins

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1-Methylphenanthro[3,4-b]thiophene: Determination of the tertiary structure in solution and in the crystalline state by NMR spectroscopy and X-ray diffraction

Journal of Heterocyclic Chemistry ◽

10.1002/jhet.5570220268 ◽

1985 ◽

Vol 22 (2) ◽

pp. 545-553 ◽

Cited By ~ 11

Author(s):

M. J. Musmar ◽

Gary E. Martin ◽

Robert T. Gampe ◽

Vincent M. Lynch ◽

Stanley H. Simonsen ◽

...

Keyword(s):

Nmr Spectroscopy ◽

Crystalline State ◽

Tertiary Structure ◽

X Ray Diffraction ◽

X Ray ◽

Structure In Solution

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High-Resolution Single-Molecule FRET via DNA eXchange (FRET X)

10.1101/2020.10.15.340885 ◽

2020 ◽

Author(s):

Mike Filius ◽

Sung Hyun Kim ◽

Ivo Severins ◽

Chirlmin Joo

Keyword(s):

Structural Analysis ◽

High Resolution ◽

Single Molecule ◽

Single Object ◽

Single Molecule Fret ◽

Dna Strands ◽

Versatile Tool ◽

Fret Efficiency ◽

Fret Pair

ABSTRACTSingle-molecule FRET is a versatile tool to study nucleic acids and proteins at the nanometer scale. However, currently, only a couple of FRET pairs can be reliably measured on a single object. The limited number of available FRET pair fluorophores and complicated data analysis makes it challenging to apply single-molecule FRET for structural analysis of biomolecules. Currently, only a couple of FRET pairs can be reliably measured on a single object. Here we present an approach that allows for the determination of multiple distances between FRET pairs in a single object. We use programmable, transient binding between short DNA strands to resolve the FRET efficiency of multiple fluorophore pairs. By allowing only a single FRET pair to be formed at a time, we can determine the FRET efficiency and pair distance with sub-nanometer resolution. We determine the distance between other pairs by sequentially exchanging DNA strands. We name this multiplexing approach FRET X for FRET via DNA eXchange. We envision that our FRET X technology will be a tool for the high-resolution structural analysis of biomolecules and other nano-structures.

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X-ray determination of static displacements of atoms in alloyed Ni3Al

Journal of Applied Crystallography ◽

10.1107/s0021889887008975 ◽

1988 ◽

Vol 21 (1) ◽

pp. 41-47 ◽

Cited By ~ 15

Author(s):

M. Morinaga ◽

K. Sone ◽

T. Kamimura ◽

K. Ohtaka ◽

N. Yukawa

Keyword(s):

Structural Analysis ◽

Atomic Radius ◽

Lattice Points ◽

Alloying Elements ◽

Alloying Element ◽

X Ray ◽

Atomic Displacements ◽

Interesting Correlation ◽

Average Lattice

Single crystals of Ni3(Al, M) were grown by the Bridgman method, where M is Ti, V, Cr, Mn, Fe, Nb, Mo and Ta. The composition was controlled to be about Ni75Al20 M 5 so that the alloying element, M, substitutes mainly for Al. With these crystals conventional X-ray structural analysis was performed. The measured static displacements of atoms from the average lattice points depended largely on the alloying elements and varied in the range 0.00–0.13 Å for Ni atoms and 0.09–0.18 Å for Al atoms. It was found that these atomic displacements correlated well with the atomic radius of the alloying element, M. For example, when the atomic radius of M is larger than that of Al, the static displacements are large for the atoms in the Al sublattice but small for the atoms in the Ni sublattice. By contrast, when the atomic radius of M is smaller than that of Al, the displacements are more enhanced in the Ni sublattice than in the Al sublattice. Thus, there is an interesting correlation between the atomic displacements in both the Al and Ni sublattices in the presence of alloying elements. This seems to be one of the characteristics of alloyed compounds with several sublattices.

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