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

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.

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

Bioinformatics ◽

10.1093/bioinformatics/btz579 ◽

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.

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Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

Protein and Peptide Letters ◽

10.2174/0929866526666181128141953 ◽

2019 ◽

Vol 26 (1) ◽

pp. 35-43 ◽

Cited By ~ 3

Author(s):

Natalie K. Garcia ◽

Galahad Deperalta ◽

Aaron T. Wecksler

Keyword(s):

Mass Spectrometry ◽

Protein Structure ◽

Protein Interactions ◽

Quaternary Structure ◽

Solvent Accessibility ◽

Higher Order ◽

Structure Characterization ◽

Order Structure ◽

Protein Footprinting ◽

Wide Range

Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. Conclusion: Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

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Direct detection of the protein quaternary structure and denatured entity by small-angle scattering: guanidine hydrochloride denaturation of chaperonin protein GroEL

Journal of Applied Crystallography ◽

10.1107/s002188980101473x ◽

2002 ◽

Vol 35 (1) ◽

pp. 1-7 ◽

Cited By ~ 9

Author(s):

Yuzuru Hiragi ◽

Yasutaka Seki ◽

Kaoru Ichimura ◽

Kunitsugu Soda

Keyword(s):

Small Angle ◽

Quaternary Structure ◽

Direct Detection ◽

Guanidine Hydrochloride ◽

Average Molecular Weight ◽

Higher Order ◽

Small Angle Scattering ◽

Radius Of Gyration ◽

Order Structure ◽

Angle Scattering

A change in the higher-order structure of an oligomeric protein is directly detectable by small-angle scattering. A small-angle X-ray scattering (SAXS) study of the denaturation process of the chaperonin protein GroEL by guanidine hydrochloride (GdnHCl) showed that the disappearance of the quaternary structure can be monitored by using a Kratky plot of the scattered intensities, demonstrating the advantage of the SAXS method over other indirect methods, such as light scattering, circular dichroism (CD), fluorescence and sedimentation. The collapse of the quaternary structure was detected at a GdnHCl concentration of 0.8 Mfor a solution containing ADP (adenosine diphosphate)/Mg2+(2 mM)/K+. From pairwise plots of the change in forward scattering intensityJ(0)/C(weight-average molecular weight) and thez-average (root mean square) radius of gyration against the GdnHCl concentration, the stability and nature of the denatured protein can be determined. The SAXS results suggest that the GroEL tetradecamer directly dissociates to the unfolded coil without going through a globular monomer state. The denatured ensemble is not a single unfolded monomer coil particle, but some mixture of entangled aggregates and a monomer of the coil molecules. Small-angle scattering is a powerful method for the detection and study of changes in quaternary and higher-order structures of oligomeric proteins.

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Use of the Amide II Infrared Band of Proteins for Secondary Structure Determination and Comparability of Higher Order Structure

Current Pharmaceutical Biotechnology ◽

10.2174/1389201015666141012181609 ◽

2014 ◽

Vol 15 (9) ◽

pp. 880-889 ◽

Cited By ~ 10

Author(s):

Brian Murphy ◽

Jennifer D'Antonio ◽

Mark Manning ◽

Wasfi Al-Azzam

Keyword(s):

Secondary Structure ◽

Structure Determination ◽

Higher Order ◽

Order Structure ◽

Infrared Band

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The chemical reactions of the haemagglutinins and neuraminidases of different strains of influenza viruses: II. Effects of reagents modifying the higher order structure of the protein molecule

Journal of Hygiene ◽

10.1017/s002217240004170x ◽

1969 ◽

Vol 67 (2) ◽

pp. 301-310 ◽

Cited By ~ 6

Author(s):

L. Hoyle

Keyword(s):

Influenza Virus ◽

Chemical Reactions ◽

Mercuric Chloride ◽

Tertiary Structure ◽

Quaternary Structure ◽

Higher Order ◽

Influenza Viruses ◽

Order Structure ◽

Neuraminidase Activity ◽

Different Strains

SUMMARYThe results of treatment of influenza virus strains with chemical reagents acting on the higher-order structure of protein molecules shows that both the haemagglutinating and enzymic activities are susceptible to these agents but there are considerable differences between the different strains and the neuraminidase activity is more sensitive than the haemagglutinating activity.The neuraminidase activity of A and A1strains is destroyed by urea, guanidine, urea+dithiothreitol and mercuric chloride. The haemagglutinin of the PR 8 and SWINE strains is resistant to urea and mercuric chloride but destroyed by guanidine and by urea+dithiothreitol. The haemagglutinin of the DSP strain of virus A and the A1strains is resistant to urea, guanidine and mercuric chloride but is destroyed by urea+dithiothreitol.The neuraminidase activity of the A2strains is more resistant than that of the A and A1strains. It is resistant to mercuric chloride and partially resistant to urea but is destroyed by guanidine and by urea+dithiothreitol. The A2haemagglutinin is resistant to urea, urea+dithiothreitol, and mercuric chloride but is destroyed by guanidine.The LEE virus neuraminidase is resistant to urea and partially resistant to guanidine but is destroyed by urea+dithiothreitol and mercuric chloride. The LEE haemagglutinin is resistant to urea, guanidine and mercuric chloride but is destroyed by urea+dithiothreitol.It is suggested that the surface projections of the virus particle are protein polymers each made up of three or four monomers which are the components of the V antigen complex. Antigenic activity is a function of the primary or secondary structure of the monomers, haemagglutinin activity is a function of the tertiary structure of the monomers, while neuraminidase activity is a function of the quaternary structure of the polymer.From studies of the chemical reactions of their haemagglutinins and neuraminidases strains of influenza virus A can be classified into groups. These groups are very similar to but not precisely identical with groupings made by serological methods.

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Protein higher-order-structure determination by fast photochemical oxidation of proteins and mass spectrometry analysis

Nature Protocols ◽

10.1038/s41596-020-0396-3 ◽

2020 ◽

Vol 15 (12) ◽

pp. 3942-3970

Author(s):

Xiaoran Roger Liu ◽

Don L. Rempel ◽

Michael L. Gross

Keyword(s):

Mass Spectrometry ◽

Structure Determination ◽

Higher Order ◽

Photochemical Oxidation ◽

Mass Spectrometry Analysis ◽

Order Structure ◽

Spectrometry Analysis

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Distance-based Reconstruction of Protein Quaternary Structures from Inter-Chain Contacts

10.22541/au.162696617.75074967/v1 ◽

2021 ◽

Author(s):

Elham Soltanikazemi ◽

Farhan Quadir ◽

Raj Roy ◽

Jianlin Cheng

Keyword(s):

Quaternary Structure ◽

Structural Models ◽

Simulation Method ◽

Contact Density ◽

High Quality ◽

Contact Prediction ◽

Residue Contact ◽

Protein Dimers ◽

Distance Restraints ◽

Quaternary Structures

Predicting the quaternary structure of protein complex is an important problem. Inter-chain residue-residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures. However, few methods have been developed to build quaternary structures from predicted inter-chain contacts. Here, we introduce a gradient descent optimization algorithm (GD) to build quaternary structures of protein dimers utilizing inter-chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true or predicted contacts. GD consistently performs better than a simulated annealing method and a Markov Chain Monte Carlo simulation method. Using true inter-chain contacts as input, GD can reconstruct high-quality structural models for homodimers and heterodimers with average TM-score ranging from 0.92 to 0.99 and average interface root mean square distance (I-RMSD) from 0.72 Å to 1.64 Å. On a dataset of 115 homodimers, using predicted inter-chain contacts as input, the average TM-score of the structural models built by GD is 0.76. For 46% of the homodimers, high-quality structural models with TM-score >= 0.9 are reconstructed from predicted contacts. There is a strong correlation between the quality of the reconstructed models and the precision and recall of predicted contacts. If the precision or recall of predicted contacts is >20%, GD can reconstruct good models for most homodimers, indicating only a moderate precision or recall of inter-chain contact prediction is needed to build good structural models for most homodimers. Moreover, the accuracy of reconstructed models positively correlates with the contact density in dimers.

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Dectin-1 Molecular Aggregation and Signaling is Sensitive to β-Glucan Structure and Glucan Exposure on Candida albicans Cell Walls

10.1101/824995 ◽

2019 ◽

Author(s):

Eduardo U. Anaya ◽

Akram Etemadi Amin ◽

Michael J. Wester ◽

Michael E. Danielson ◽

Kyle S. Michel ◽

...

Keyword(s):

Cell Walls ◽

Quaternary Structure ◽

Calcium Influx ◽

Particle Surface ◽

Higher Order ◽

Receptor Modeling ◽

Random Coil ◽

Order Structure ◽

Resting Cells ◽

Molecular Aggregation

AbstractDectin-1A is a C-type Lectin innate immunoreceptor that recognizes β-(1,3;1,6)-glucan, a structural component of Candida species cell walls. The higher order structure of β-glucans ranges from random coil to insoluble fiber due to varying degrees of tertiary (helical) and quaternary structure. Model Saccharomyces cerevisiae β-glucans of medium and high molecular weight (MMW and HMW, respectively) are highly structured. In contrast, low MW glucan (LMW) is much less structured. Despite similar affinity for Dectin-1A, the ability of glucans to induce Dectin-1A mediated calcium influx and Syk phosphorylation positively correlates with their degree of higher order structure. Chemical denaturation and renaturation of MMW glucan showed that glucan structure determines agonistic potential, but not binding affinity, for Dectin-1A. We explored the role of glucan structure on Dectin-1A oligomerization, which is thought to be required for Dectin-1 signaling. Glucan signaling decreased Dectin-1A diffusion coefficient in inverse proportion to glucan structural content, which was consistent with Dectin-1A aggregation. Förster Resonance Energy Transfer (FRET) measurements revealed that molecular aggregation of Dectin-1 occurs in a manner dependent upon glucan higher order structure. Number and Brightness analysis specifically confirmed an increase in the Dectin-1A dimer and oligomer populations that is correlated with glucan structure content. Comparison of receptor modeling data with FRET measurements confirms that in resting cells, Dectin-1A is predominantly in a monomeric state. Super Resolution Microscopy revealed that glucan-stimulated Dectin-1 aggregates are very small (<15 nm) collections of a few engaged receptors. Finally, FRET measurements confirmed increased molecular aggregation of Dectin-1A at fungal particle contact sites in a manner that positively correlated with the degree of exposed glucan on the particle surface. These results indicate that Dectin-1A senses the solution conformation of β-glucans through their varying ability to drive receptor dimer/oligomer formation and activation of membrane proximal signaling events.

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