scholarly journals DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing

2019 ◽  
Author(s):  
Justin Chan ◽  
Jinhao Zou ◽  
Christopher Llynard Ortiz ◽  
Chi-Hong Chang Chien ◽  
Rong-Long Pan ◽  
...  
Keyword(s):  
Structure Determination ◽  
Quaternary Structure ◽  
Transmembrane Proteins ◽  
Supplementary Information ◽  
Order Structure ◽  
Structure Modeling ◽  
Cyclic Symmetry ◽  
X Ray ◽  
Distance Restraints ◽  
Symmetric Complex

Abstract Motivation Quaternary structure determination for transmembrane/soluble proteins requires a reliable computational protocol that leverages observed distance restraints and/or cyclic symmetry (Cn symmetry) found in most homo-oligomeric transmembrane proteins. Results We survey 118 X-ray crystallographically solved structures of homo-oligomeric transmembrane proteins (HoTPs) and find that ∼97% are Cn symmetric. Given the prevalence of Cn symmetric HoTPs and the benefits of incorporating geometry restraints in aiding quaternary structure determination, we introduce two new filters, the distance-restraints (DR) and the Symmetry-Imposed Packing (SIP) filters. SIP relies on a new method that can rebuild the closest ideal Cn symmetric complex from docking poses containing a homo-dimer without prior knowledge of the number (n) of monomers. Using only the geometrical filter, SIP, near-native poses of 7 HoTPs in their monomeric states can be correctly identified in the top-10 for 71% of all cases, or 29% among 31 HoTP structures obtained through homology modeling, while ZDOCK alone returns 14 and 3%, respectively. When the n is given, the optional n-mer filter is applied with SIP and returns the near-native poses for 76% of the test set within the top-10, outperforming M-ZDOCK’s 55% and Sam’s 47%. While applying only SIP to three HoTPs that comes with distance restraints, we found the near-native poses were ranked 1st, 1st and 10th among 54 000 possible decoys. The results are further improved to 1st, 1st and 3rd when both DR and SIP filters are used. By applying only DR, a soluble system with distance restraints is recovered at the 1st-ranked pose. Availability and implementation https://github.com/capslockwizard/drsip. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals DR-SIP: Protocols for Higher Order Structure Modeling with Distance Restraints- and Cyclic Symmetry-Imposed Packing

2018 ◽  
Author(s):  
Justin Chan ◽  
Jinhao Zou ◽  
Chi-Hong Chang Chien ◽  
Rong-Long Pan ◽  
Lee-Wei Yang
Keyword(s):  
Structure Determination ◽  
Quaternary Structure ◽  
Transmembrane Proteins ◽  
Computational Prediction ◽  
Higher Order ◽  
The Other ◽  
Order Structure ◽  
Cyclic Symmetry ◽  
Distance Restraints ◽  
Quaternary Structures

Motivation: Quaternary structure determination for proteins is difficult especially for transmembrane proteins. Even if the monomeric constituents of complexes have been experimentally resolved, computational prediction of quaternary structures is a challenging task particularly for higher order complexes. It is essential to have a reliable computational protocol to predict quaternary structures of both transmembrane and soluble proteins leveraging experimentally determined distance restraints and/or cyclic symmetry (Cn symmetry) found in most homo-oligomeric transmembrane proteins. Results: We survey 115 X-ray crystallographically solved structures of homo-oligomeric transmembrane proteins (HoTPs) to discover that 90% of them are Cn symmetric. Given the prevalence of Cn symmetric HoTPs and the benefits of incorporating geometry restraints in aiding quaternary structure determination, we introduce two new filters, the distance-restraints (DR) filter and the Symmetry-Imposed Packing (SIP) filter which takes advantage of the statistically derived tilt angle cutoff and the Cn symmetry of HoTPs without prior knowledge of the number ("n") of monomers. Using only the geometrical filter, SIP, near-native poses of the 115 HoTPs can be correctly identified in the top-5 for 52% of all cases, or 49% among the HoTPs having an n>2 (~60% of the dataset), while ZDOCK alone returns 41% and 24%, respectively. Applying only SIP to three HoTPs with distance restraints, the near-native poses for two HoTPs are ranked 1st and the other 7th among 54,000 possible decoys. With both filters, the two remain 1st while the other improved to 2nd. While a soluble system with distance restraints is recovered at the 1st-ranked pose by applying only DR.

Parakeet hemoglobin – its crystal structure and oxygen affinity in relation to some avian hemoglobins

2020 ◽  
Vol 27 ◽  
Author(s):  
S.M. Jaimohan ◽  
M.D. Naresh ◽  
A.B. Mandal
Keyword(s):  
Structure Determination ◽  
Model Building ◽  
Tertiary Structure ◽  
Quaternary Structure ◽  
Oxygen Affinity ◽  
Diffusion Method ◽  
Data Set ◽  
X Ray ◽  
Loop Region ◽  
Psittacula Krameri

Background: “Avians” often show efficient oxygen management to meet the demands of their metabolism. Hemoglobin, a transporter protein consists of four non-covalently linked subunits contain haem binding hydrophobic pocket serves as a site of allosteric cooperativity. The physiology and anatomy of both mammals and avian are functionally different, in birds, the respiratory system formed by small air sacs that serve as tidal ventilation for the lungs and have no significant exchange across their cells. Parakeet (Psittacula Krameri) a tropical and non-migrating species and it is easily adapted to living in disturbed habitat. The sequence analysis reveals that α and β chain of parakeet hemoglobin highly similar grey lag goose and bar headed goose hemoglobin respectively. Thus it has been tempted us to study in to analyzing the sequence and structural comparison of this hemoglobin to find out the physiological capabilities of parakeet hemoglobin. Objective: The structure determination studies of parakeet hemoglobin by X-ray diffraction. The sequence and structure are compared with goose, chicken and human Hb, emphasizing the role of amino acids in the subunit contacts that facilitate survival by low oxygen demand. Methods: The Hb was purified and crystallized by hanging drop vapor diffusion method using poly ethylene glycol (PEG) 3350 and sodium phosphate buffer. X-ray diffracted data set was collected at 3Å resolution, the data was processed in Automar and molecular replacement, refinements, model building was carried out in CCP4i program package. The final refined model was deposited in protein data bank with accession id 2zfb. Results: The tertiary structure of Parakeet Hb is compared with the met form of BHG Hb (1c40) and oxy form of GLG (1faw) and oxy form of human Hbs (1hho). Superimposing parakeet Hb α1β1 subunit with ‘R’ state human Hb shows an r.m.s.d of 0.98 Å and for BHG and GLG Hb, the r.m.s.d shows 0.72 and 0.61 Å. The replacement of α115Asp in parakeet Hb as against the α115Glu in human Hb results in the movement of GH corners. The amino acid proline at α50 present only in Parakeet Hb and Chicken HbD and not present in any other avian family which includes human Hb. The residue α78Thr located in EF corner loop region, which slightly diverge when superimposing with human and BHG Hb and also replacement of α113Asn present only in Parakeet Hb placed near the FG helix corner. Conclusion: The present study describes the structure determination of parakeet hemoglobin and its structural features to understand its oxygen affinity characteristics. The crystals were obtained by buffered low-salt conditions, like those of chicken HbD, carbonmonoxy and cyanomet human Hb. The present study reveals several interesting and unique modifications in the finer aspects of the quaternary structure of parakeet Hb, which are involved in oxygen affinity characteristics and the α1β1 subunit contacts. Crystallization of parakeet Hb with allosteric effectors like Inositol pentaphosphate may bring further understanding of the influence of physiological and environmental factors on the quaternary structure.

scholarly journals The TMCrys server for supporting crystallization of transmembrane proteins

2019 ◽  
Vol 35 (20) ◽  
pp. 4203-4204
Author(s):  
Julia K Varga ◽  
Gábor E Tusnády
Keyword(s):  
Membrane Proteins ◽  
Structure Determination ◽  
Web Server ◽  
Transmembrane Proteins ◽  
Prediction Method ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Successful Completion ◽  
Determination Process

Abstract Motivation Due to their special properties, the structures of transmembrane proteins are extremely hard to determine. Several methods exist to predict the propensity of successful completion of the structure determination process. However, available predictors incorporate data of any kind of proteins, hence they can hardly differentiate between crystallizable and non-crystallizable membrane proteins. Results We implemented a web server to simplify running TMCrys prediction method that was developed specifically to separate crystallizable and non-crystallizable membrane proteins. Availability and implementation http://tmcrys.enzim.ttk.mta.hu Supplementary information Supplementary data are available at Bioinformatics online.

Quaternary structure of Limulus polyphemus hemocyanin

1978 ◽  
Vol 36 (2) ◽  
pp. 176-177
Author(s):  
T. Wichertjes ◽  
E.J. Kwak ◽  
E.F.J. Van Bruggen
Keyword(s):  
Electron Microscopy ◽  
Functional Properties ◽  
Horseshoe Crab ◽  
Temperature Jump ◽  
Quaternary Structure ◽  
Crystallographic Analysis ◽  
Limulus Polyphemus ◽  
Oxygen Binding ◽  
X Ray ◽  
Intact Molecule

Hemocyanin of the horseshoe crab (Limulus polyphemus) has been studied in nany ways. Recently the structure, dissociation and reassembly was studied using electron microscopy of negatively stained specimens as the method of investigation. Crystallization of the protein proved to be possible and X-ray crystallographic analysis was started. Also fluorescence properties of the hemocyanin after dialysis against Tris-glycine buffer + 0.01 M EDTA pH 8.9 (so called “stripped” hemocyanin) and its fractions II and V were studied, as well as functional properties of the fractions by NMR. Finally the temperature-jump method was used for assaying the oxygen binding of the dissociating molecule and of preparations of isolated subunits. Nevertheless very little is known about the structure of the intact molecule. Schutter et al. suggested that the molecule possibly consists of two halves, combined in a staggered way, the halves themselves consisting of four subunits arranged in a square.

A study on α-RuCl3 crystal structure by scanning tunneling microscopy

1989 ◽  
Vol 47 ◽  
pp. 30-31
Author(s):  
H.-J. Cantow ◽  
H. Hillebrecht ◽  
S. Magonov ◽  
H. W. Rotter ◽  
G. Thiele
Keyword(s):  
Crystal Structure ◽  
Density Distribution ◽  
Scanning Tunneling Microscopy ◽  
Electron Density ◽  
Structure Determination ◽  
Electron Density Distribution ◽  
Scanning Tunneling ◽  
Monoclinic Space Group ◽  
Tunneling Microscopy ◽  
X Ray

From X-ray analysis, the conclusions are drawn from averaged molecular informations. Thus, limitations are caused when analyzing systems whose symmetry is reduced due to interatomic interactions. In contrast, scanning tunneling microscopy (STM) directly images atomic scale surface electron density distribution, with a resolution up to fractions of Angstrom units. The crucial point is the correlation between the electron density distribution and the localization of individual atoms, which is reasonable in many cases. Thus, the use of STM images for crystal structure determination may be permitted. We tried to apply RuCl3 - a layered material with semiconductive properties - for such STM studies. From the X-ray analysis it has been assumed that α-form of this compound crystallizes in the monoclinic space group C2/m (AICI3 type). The chlorine atoms form an almost undistorted cubic closed package while Ru occupies 2/3 of the octahedral holes in every second layer building up a plane hexagon net (graphite net). Idealizing the arrangement of the chlorines a hexagonal symmetry would be expected. X-ray structure determination of isotypic compounds e.g. IrBr3 leads only to averaged positions of the metal atoms as there exist extended stacking faults of the metal layers.

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