scholarly journals The three-dimensional structure of supercoiled deoxyribonucleic acid in solution. Evidence obtained from the angular distribution of scattered light

1972 ◽  
Vol 128 (3) ◽  
pp. 569-578 ◽  
Author(s):  
Douglas J. Jolly ◽  
Ailsa M. Campbell
Keyword(s):  
Light Scattering ◽  
Deoxyribonucleic Acid ◽  
Scattered Light ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Mean Square ◽  
Circular Dna ◽  
Three Dimensional Models ◽  
Experimental Findings

1. The size and shape of superhelical double-stranded circular DNA from bacteriophage ØX174 were investigated by light-scattering. The molecular weight of the DNA is 3.17×106 and the root-mean-square radius is 103.5nm. 2. The light-scattering envelopes of various theoretical three-dimensional models for such DNA molecules were calculated by repetitive computational techniques, and the results were compared with the experimental findings. 3. It is concluded that the structure of supercoiled DNA containing -12 superhelical turns in buffer of I0.2 corresponds best to one of the more compact models for superhelix structure such as the branched model, and the commonly employed straight interwound superhelix model is incompatible with the experimental results, at the superhelix density found.

scholarly journals Protein Folding: Search for Basic Physical Models

2003 ◽  
Vol 3 ◽  
pp. 623-635 ◽  
Author(s):  
Ivan Y. Torshin ◽  
Robert W. Harrison
Keyword(s):  
Protein Folding ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Physical Models ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Linear Sequence ◽  
Physical Forces

How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context ofin vivoprotein folding (which has been studied only for a few proteins), the roles of the fundamental physical forces in thein vitrofolding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces). Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

IN SEARCH OF THE PROTEIN NATIVE STATE WITH A PROBABILISTIC SAMPLING APPROACH

2011 ◽  
Vol 09 (03) ◽  
pp. 383-398 ◽  
Author(s):  
BRIAN OLSON ◽  
KEVIN MOLLOY ◽  
AMARDA SHEHU
Keyword(s):  
Structure Prediction ◽  
Computational Models ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Search Space ◽  
Conformational Space ◽  
Conformational Search ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Native State

The three-dimensional structure of a protein is a key determinant of its biological function. Given the cost and time required to acquire this structure through experimental means, computational models are necessary to complement wet-lab efforts. Many computational techniques exist for navigating the high-dimensional protein conformational search space, which is explored for low-energy conformations that comprise a protein's native states. This work proposes two strategies to enhance the sampling of conformations near the native state. An enhanced fragment library with greater structural diversity is used to expand the search space in the context of fragment-based assembly. To manage the increased complexity of the search space, only a representative subset of the sampled conformations is retained to further guide the search towards the native state. Our results make the case that these two strategies greatly enhance the sampling of the conformational space near the native state. A detailed comparative analysis shows that our approach performs as well as state-of-the-art ab initio structure prediction protocols.

scholarly journals Folding membrane proteins by deep transfer learning

2017 ◽  
Author(s):  
Sheng Wang ◽  
Zhen Li ◽  
Yizhou Yu ◽  
Jinbo Xu
Keyword(s):  
Membrane Proteins ◽  
Transfer Learning ◽  
Prediction Accuracy ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Blind Test ◽  
Distance Restraints ◽  
Dimensional Models ◽  
Three Dimensional Models ◽  
Better Than

SummaryComputational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts MP contacts by learning from non-membrane proteins (non-MPs) and then predicting three-dimensional structure models using the predicted contacts as distance restraints. Tested on 510 non-redundant MPs, our method has contact prediction accuracy at least 0.18 better than existing methods, predicts correct folds for 218 MPs (TMscore>0.6), and generates three-dimensional models with RMSD less than 4Å and 5Å for 57 and 108 MPs, respectively. A rigorous blind test in the continuous automated model evaluation (CAMEO) project shows that our method predicted high-resolution three-dimensional models for two recent test MPs of 210 residues with RMSD ∼2Å. We estimated that our method could predict correct folds for 1,345–1,871 reviewed human multi-pass MPs including a few hundred new folds, which shall facilitate the discovery of drugs targeting at membrane proteins.

scholarly journals Light-scattering studies on deoxyribonucleic acid flexibility. The solution properties of a small circular deoxyribonucleic acid molecule

1972 ◽  
Vol 130 (4) ◽  
pp. 1019-1028 ◽  
Author(s):  
Douglas J. Jolly ◽  
Ailsa M. Campbell
Keyword(s):  
Light Scattering ◽  
Deoxyribonucleic Acid ◽  
Persistence Length ◽  
Resolving Power ◽  
Experimental Investigations ◽  
Volume Factor ◽  
Circular Dna ◽  
Dna Molecule ◽  
Double Stranded Dna ◽  
Infected Cells

Previous investigations on the persistence length of DNA in solution have revealed large discrepancies between hydrodynamic results and those from light-scattering techniques which have potentially a greater resolving power. The information obtained from experiments on a small circular DNA molecule has resolved these discrepancies. The non-superhelical circular double-stranded DNA molecule from bacteriophage [unk]X174-infected cells is small enough to permit accurate light-scattering extrapolations, and its solutions have negligible anisotropy. The persistence length obtained from experimental investigations on this molecule is comparable with that obtained by hydrodynamic techniques, even with variation of the excluded-volume factor.

scholarly journals Conformational analysis of deoxyribonucleic acid from PM2 bacteriophage. The effect of size on supercoil shape

1976 ◽  
Vol 155 (1) ◽  
pp. 101-105 ◽  
Author(s):  
A M Campbell
Keyword(s):  
Light Scattering ◽  
Ionic Strength ◽  
Deoxyribonucleic Acid ◽  
Laser Light ◽  
Structural Models ◽  
Laser Light Scattering ◽  
Mean Square ◽  
Planar Molecule ◽  
The One ◽  
Experimental Interference

Laser light-scattering studies of bacteriophage PM2 DNA showed the molecule to have mol.wt. 5.9 } 10(6) and root-mean -square radius 125 nm at an ionic strength of 0.2 mol/litre. Computer-generated curves compatible with these data were compared with the experimental interference curve for several structural models of the molecules. The data fit best to an asymmetric four-armed planar molecule in which all four arms emerge from or close to the one area of the molecule. This contrasts with the smaller DNA molecules investigated, which have shown a three-armed molecule, whose symmetry varies with primary structure.

scholarly journals SERIAL RECONSTRUCTION OF THE CHARACTERISTIC GRANULE OF THE LANGERHANS CELL

1968 ◽  
Vol 36 (3) ◽  
pp. 595-602 ◽  
Author(s):  
Richard W. Sagebiel ◽  
Thomas H. Reed
Keyword(s):  
Electron Microscope ◽  
Electron Micrographs ◽  
Three Dimensional ◽  
Langerhans Cell ◽  
Human Epidermis ◽  
Dimensional Structure ◽  
Serial Sections ◽  
Three Dimensional Structure ◽  
Three Dimensional Models ◽  
The Many

Three-dimensional models of individual granules in the same Langerhans cell were made after analyzing serial sections of human epidermis in the electron microscope. These models revealed that the granule is made up of a flattened or curved orthogonal net of particles which is bounded externally by a limiting membrane and which may be disc-shaped, cup-shaped, or combinations of both shapes. This variety of shapes accounts for the many configurations of the granule seen in individual electron micrographs. Usually, the granule has a vesicular portion at, or near one margin. This demonstration of the three-dimensional structure of the granule establishes the inaccuracy of previously used descriptive terms, the granule should be called simply the "Langerhans cell granule."

Computational Advances and Enabling Technologies for 3D Microscopies in Biology

1997 ◽  
Vol 3 (S2) ◽  
pp. 1135-1136
Author(s):  
Gina Sosinsky ◽  
Mark Ellisman
Keyword(s):  
Electron Tomography ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Single Particle Reconstruction ◽  
Reconstruction Methods ◽  
Technological Advances ◽  
Biological Structures ◽  
Dimensional Reconstruction ◽  
Computational Reconstruction

Approaches for exploration of biological structures with modern 3D microscopy techniques are expanding rapidly. These technological advances include not only the imaging of structures, but also the computational reconstruction methods for calculating three-dimensional structures. The computational techniques used to investigate the three-dimensional structure of macromolecular complexes, organelles or cells include crystallographic reconstruction, helical reconstruction, icosahedral reconstruction, single particle reconstruction, electron tomography and serial section reconstruction. These techniques have particularly useful in determining structures which are too small for light microscopy or too large for NMR or X-Ray structure determination or structures for which crystals are not available or order in the crystals is limited.Advances in microscopes and associated computational capabilities have been substantial over the last few years. In this session, presentations will examine technical aspects and methods for three-dimensional reconstruction of biological structures from images acquired by electron microscopy and analyzed using the computational reconstruction techniques listed above.

Cryo-Electron Microscopy of Spiroplasma Virus SpV4

1997 ◽  
Vol 3 (S2) ◽  
pp. 87-88
Author(s):  
P.R. Chipman ◽  
R. Mckenna ◽  
J. Renaudin ◽  
T.S. Baker
Keyword(s):  
Electron Microscopy ◽  
Cross Section ◽  
Outer Surface ◽  
Average Distance ◽  
Three Dimensional ◽  
Longitudinal Axis ◽  
Lytic Cycle ◽  
Dimensional Structure ◽  
Circular Dna ◽  
Cryo Electron Microscopy

Spiroplasma, a wall-free prokaryote of the class Mollicutes, is host to a small, naked, single-stranded DNA, isometric virus. Spiroplasma virus SpV4 belongs to the Microviridae family, members of which are non-enveloped, have icosahedral capsids, release progeny through a lytic cycle, and contain circular DNA.Measurements obtained from negatively stained SpV4 particles revealed a nucleocapsid of 27nm in diameter (figure 1). The three-dimensional structure reported here, obtained from unstained particles suspended in a layer of vitreous ice (figure 2), is in agreement with these earlier results, suggesting a 27nm average distance through the nucleocapsid (figure 3). Unreported in earlier studies is the presence of a 6nm, mushroom-shaped protrusion (made up of a stalk, 2.3nm long and 1.3nm wide, and a globular bud of dimensions ≈4.0×4.0×3.7nm) stemming from an ≈1.5nm deep depression at each of the 3-fold icosahedral axes of the virion. A cross section through the longitudinal axis of one protuberance (figure 4) reveals a cylindrical dimple (≈1.0nm in diameter and 2.3nm deep), originating on the axis of the outer surface of the globular bud domain.

scholarly journals PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Adeel Malik ◽  
Ahmad Firoz ◽  
Vivekanand Jha ◽  
Shandar Ahmad
Keyword(s):  
Binding Sites ◽  
De Novo ◽  
Solvent Accessibility ◽  
Protein Structures ◽  
Three Dimensional ◽  
Data Bank ◽  
Dimensional Structure ◽  
Carbohydrate Binding ◽  
Structural And Functional Properties ◽  
Three Dimensional Models

Understanding of the three-dimensional structures of proteins that interact with carbohydrates covalently (glycoproteins) as well as noncovalently (protein-carbohydrate complexes) is essential to many biological processes and plays a significant role in normal and disease-associated functions. It is important to have a central repository of knowledge available about these protein-carbohydrate complexes as well as preprocessed data of predicted structures. This can be significantly enhanced by tools de novo which can predict carbohydrate-binding sites for proteins in the absence of structure of experimentally known binding site. PROCARB is an open-access database comprising three independently working components, namely, (i) Core PROCARB module, consisting of three-dimensional structures of protein-carbohydrate complexes taken from Protein Data Bank (PDB), (ii) Homology Models module, consisting of manually developed three-dimensional models of N-linked and O-linked glycoproteins of unknown three-dimensional structure, and (iii) CBS-Pred prediction module, consisting of web servers to predict carbohydrate-binding sites using single sequence or server-generated PSSM. Several precomputed structural and functional properties of complexes are also included in the database for quick analysis. In particular, information about function, secondary structure, solvent accessibility, hydrogen bonds and literature reference, and so forth, is included. In addition, each protein in the database is mapped to Uniprot, Pfam, PDB, and so forth.

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