AB INITIO CALCULATIONS OF THE ELECTRONIC STRUCTURES AND BIOLOGICAL FUNCTIONS OF PROTEIN MOLECULES

2002 ◽  
Vol 16 (30) ◽  
pp. 1151-1162 ◽  
Author(s):  
HAOPING ZHENG
Keyword(s):  
Ab Initio ◽  
Trypsin Inhibitor ◽  
Electronic Structures ◽  
Biological Function ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Computational Effort ◽  
Biological Functions ◽  
Protein Molecules

The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with precise calculations. Thus the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule has become a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), will be presented in this paper. The reactive sites of the inhibitors are determined and explained. The accuracy of structure determination of the inhibitors are tested theoretically.

Ab Initio Determination of a New Complex Structure (55 Non-Hydrogen Atoms) from Synchrotron Powder Data: An Uncommon Nickel Succinate, Ni7(C4H4O4)4(OH)6(H2O)3•7H2O

2004 ◽  
Vol 443-444 ◽  
pp. 333-336
Author(s):  
N. Guillou ◽  
C. Livage ◽  
W. van Beek ◽  
G. Férey
Keyword(s):  
Ab Initio ◽  
Complex Structure ◽  
Three Dimensional ◽  
Free Water ◽  
Hydrogen Atoms ◽  
Monoclinic System ◽  
Synchrotron Powder Diffraction ◽  
Chloride Hexahydrate ◽  
Autogenous Pressure

Ni7(C4H4O4)4(OH)6(H2O)3. 7H2O, a new layered nickel(II) succinate, was prepared hydrothermally (180°C, 48 h, autogenous pressure) from a 1:1.5:4.1:120 mixture of nickel (II) chloride hexahydrate, succinic acid, potassium hydroxide and water. It crystallizes in the monoclinic system (space group P21/c, Z = 4) with the following parameters a = 7.8597(1) Å, b = 18.8154(3)Å, c = 23.4377(4) Å,ϐ = 92.0288(9)°, and V = 3463.9(2) Å3. Its structure, which contains 55 non-hydrogen atoms, was solved ab initio from synchrotron powder diffraction data. It can be described from hybrid organic-inorganic layers, constructed from nickel oxide corrugated chains. These chains are built up from NiO6hexameric units connected via a seventh octahedron. Half of the succinates decorate the chains, and the others connect them to form the layers. The three dimensional arrangement is ensured by hydrogen bonds directly between two adjacent layers and via free water molecules.

scholarly journals An 1 H NMR determination of the three-dimensional structures of mirror-image forms of a Leu-5 variant of the trypsin inhibitor from Ecballium elaterium (EETI-II)

1994 ◽  
Vol 3 (2) ◽  
pp. 291-302 ◽  
Author(s):  
Katherine J. Nielsen ◽  
Dianne Alewood ◽  
John Andrews ◽  
Stephen B.H. Kent ◽  
David J. Craik
Keyword(s):  
Trypsin Inhibitor ◽  
Three Dimensional ◽  
Mirror Image ◽  
H Nmr

A Model for the Fast Determination of Modal Sound Transmission of Large Rectangular Opening

2020 ◽  
Vol 142 (6) ◽  
Author(s):  
Jiazhu Li ◽  
Rui Zhang ◽  
Shen Chen ◽  
Can Li ◽  
Jian Chen
Keyword(s):  
Wave Equations ◽  
Three Dimensional ◽  
Sound Transmission ◽  
Computational Effort ◽  
Sound Insulation ◽  
Fast Determination ◽  
High Frequencies ◽  
Higher Order Modes ◽  
Insulation Performance

Abstract The existence of openings affects the sound insulation performance of structures significantly. The determination of sound transmission through large rectangular openings is often time-consuming, because of the large number of modes, especially if there is a need to go to high frequencies. A model is proposed and detailed based on three-dimensional wave equations, the transfer matrix method, and modal superposition. The viscous and thermal boundary layer effects have been concerned; hence, the model accuracy for narrow slits was improved. The computational effort is significantly decreased by neglecting the cross-modal sound transmission. The accuracy of this model is validated by comparing it with the existing model, the measurement, and the acoustic finite element method. The study of sound transmission behavior of higher-order modes is performed. The modal sound transmission is predicted and compared for several modes. The phenomenon that is different from that of the plane wave situation is found and discussed.

scholarly journals Regulation of long non-coding RNAs and circular RNAs in spermatogonial stem cells

Reproduction ◽  
2019 ◽  
Vol 158 (1) ◽  
pp. R15-R25 ◽  
Author(s):  
Fan Zhou ◽  
Wei Chen ◽  
Yiqun Jiang ◽  
Zuping He
Keyword(s):  
Stem Cells ◽  
Biological Function ◽  
Spermatogonial Stem Cells ◽  
Circular Rnas ◽  
Biological Functions ◽  
Self Renewal ◽  
Coordinated Expression ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

Spermatogonial stem cells (SSCs) are one of the most significant stem cells with the potentials of self-renewal, differentiation, transdifferentiation and dedifferentiation, and thus, they have important applications in reproductive and regenerative medicine. They can transmit the genetic and epigenetic information across generations, which highlights the importance of the correct establishment and maintenance of epigenetic marks. Accurate transcriptional and post-transcriptional regulation is required to support the highly coordinated expression of specific genes for each step of spermatogenesis. Increasing evidence indicates that non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play essential roles in controlling gene expression and fate determination of male germ cells. These ncRNA molecules have distinct characteristics and biological functions, and they independently or cooperatively modulate the proliferation, apoptosis and differentiation of SSCs. In this review, we summarized the features, biological function and fate of mouse and human SSCs, and we compared the characteristics of lncRNAs and circRNAs. We also addressed the roles and mechanisms of lncRNAs and circRNAs in regulating mouse and human SSCs, which would add novel insights into the epigenetic mechanisms underlying mammalian spermatogenesis and provide new approaches to treat male infertility.

On Potential Energy Models for EA-based Ab Initio Protein Structure Prediction

2010 ◽  
Vol 18 (2) ◽  
pp. 255-275 ◽  
Author(s):  
Milan Mijajlovic ◽  
Mark J. Biggs ◽  
Dusan P. Djurdjevic
Keyword(s):  
Protein Structure ◽  
Potential Energy ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Three Dimensional ◽  
Free Energy Surface ◽  
Energy Models ◽  
Parameter Values

Ab initio protein structure prediction involves determination of the three-dimensional (3D) conformation of proteins on the basis of their amino acid sequence, a potential energy (PE) model that captures the physics of the interatomic interactions, and a method to search for and identify the global minimum in the PE (or free energy) surface such as an evolutionary algorithm (EA). Many PE models have been proposed over the past three decades and more. There is currently no understanding of how the behavior of an EA is affected by the PE model used. The study reported here shows that the EA behavior can be profoundly affected: the EA performance obtained when using the ECEPP PE model is significantly worse than that obtained when using the Amber, OPLS, and CVFF PE models, and the optimal EA control parameter values for the ECEPP model also differ significantly from those associated with the other models.

scholarly journals RNA 3D Structure Prediction Using Coarse-Grained Models

2021 ◽  
Vol 8 ◽  
Author(s):  
Jun Li ◽  
Shi-Jie Chen
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Biological Functions ◽  
3D Structures ◽  
Rna Molecules ◽  
Atomic Structures ◽  
Long Time

The three-dimensional (3D) structures of Ribonucleic acid (RNA) molecules are essential to understanding their various and important biological functions. However, experimental determination of the atomic structures is laborious and technically difficult. The large gap between the number of sequences and the experimentally determined structures enables the thriving development of computational approaches to modeling RNAs. However, computational methods based on all-atom simulations are intractable for large RNA systems, which demand long time simulations. Facing such a challenge, many coarse-grained (CG) models have been developed. Here, we provide a review of CG models for modeling RNA 3D structures, compare the performance of the different models, and offer insights into potential future developments.

The structure of haemoglobin VIII. A three-dimensional Fourier synthesis at 5.5 Å resolution: determination of the phase angles

1961 ◽  
Vol 265 (1320) ◽  
pp. 15-38 ◽  
Keyword(s):  
Phase Angle ◽  
Least Squares Method ◽  
Heavy Atom ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Fourier Synthesis ◽  
Shape Factors ◽  
Heavy Atoms ◽  
Phase Angles

Determination of the phase angles of a crystalline protein requires a series of isomorphous heavy-atom compounds, with heavy atoms attached to different sites on the protein molecule. The asymmetric unit of horse oxyhaem oglobin was found to combine with heavy atoms at two different sites which are now known to be sulphydryl groups. Altogether six different heavy - atom com pounds of haemoglobin were made which proved isomorphous on X -ray analysis. The positions of the heavy atoms were determined first by difference Patterson and Fourier projections on the centrosym metric plane of the monoclinic crystals, and later by three-dimensional correlation functions, ( F H 1 — F H 2 ) 2 being used as coefficients, where F H 1 and F H 2 are the structure factors of the two different heavy-atom compounds. The parameters and anisotropic shape factors of the heavy atoms were refined by a three-dimensional least-squares method. For each of the 1200 reflexions in the limiting sphere of (5.5 Å) -1 the structure amplitudes of all seven compounds were combined in an Argand diagram and the probability of the phase angle having a value a was calculated for oc = 0, 5, 10, ..., 355°. The coefficients for the final Fourier summation were then calculated in two different ways. In one method the vector from the origin to the centroid of the probability distribution, plotted around a circle of radius | F |, was chosen as the ‘best F’. The alternative set of coefficients was calculated, using the full, observed, value of F and the most probable value of the phase angle a. The most probable error in phase angle was found to be 23°, and the standard error in electron density to be expected in the final results 0.12 e/Å 3 .

Sign in / Sign up

Export Citation Format

Share Document