scholarly journals Mechanics of allostery: contrasting the induced fit and population shift scenarios

2019 ◽  
Author(s):  
Riccardo Ravasio ◽  
Solange Flatt ◽  
Le Yan ◽  
Stefano Zamuner ◽  
Carolina Brito ◽  
...  
Keyword(s):  
Proper Function ◽  
Cooperative Binding ◽  
Induced Fit ◽  
Data Set ◽  
Elastic Mode ◽  
Allosteric Proteins ◽  
Protein Size ◽  
Distant Location ◽  
Population Shift ◽  
Optimal Stiffness

In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed number of stable configurations, explain such cooperative binding from a thermodynamic viewpoint. Yet, understanding what mechanical principles constrain these models remains a challenge. Here we provide an empirical study on 34 proteins supporting the idea that allosteric conformational change generally occurs along a soft elastic mode presenting extended regions of high shear. We argue, based on a detailed analysis of how the energy profile along such a mode depends on binding, that in the induced fit scenario there is an optimal stiffness for cooperative binding, where N is the number of residues involved in the allosteric response. We find that the population shift scenario is more robust to mutation affecting stiffness, as binding becomes more and more cooperative with stiffness up to the same characteristic value , beyond which cooperativity saturates instead of decaying. We confirm numerically these findings in a non-linear mechanical model. Dynamical considerations suggest that a stiffness of order is favorable in that scenario as well, supporting that for proper function proteins must evolve a functional elastic mode that is softer as their size increases. In consistency with this view, we find a significant anticorrelation between the stiffness of the allosteric response and protein size in our data set.

Engineering an iridium-containing metal–organic molecular capsule for induced-fit geometrical conversion and dual catalysis

2016 ◽  
Vol 52 (62) ◽  
pp. 9628-9631 ◽  
Author(s):  
Xuezhao Li ◽  
Jinguo Wu ◽  
Liyong Chen ◽  
Xiaoming Zhong ◽  
Cheng He ◽  
...  
Keyword(s):  
Cooperative Binding ◽  
Induced Fit ◽  
Molecular Capsule ◽  
Metal Organic ◽  
Dual Catalysis ◽  
Carbonate Anion

Quantitative dynamic capsule–capsule conversion by cooperative binding one carbonate anion and switchable dual catalysis was achieved within an Ir2Co3-type capsule.

scholarly journals Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios

2019 ◽  
Vol 117 (10) ◽  
pp. 1954-1962 ◽  
Author(s):  
Riccardo Ravasio ◽  
Solange Marie Flatt ◽  
Le Yan ◽  
Stefano Zamuner ◽  
Carolina Brito ◽  
...  
Keyword(s):  
Induced Fit ◽  
Population Shift

Population shift vs induced fit: The case of bovine seminal ribonuclease swapping dimer

Biopolymers ◽  
2004 ◽  
Vol 73 (6) ◽  
pp. 689-695 ◽  
Author(s):  
Antonello Merlino ◽  
Luigi Vitagliano ◽  
Filomena Sica ◽  
Adriana Zagari ◽  
Lelio Mazzarella
Keyword(s):  
Induced Fit ◽  
Bovine Seminal Ribonuclease ◽  
Population Shift

scholarly journals Simple estimation of surface roughness parameters from single level sonic anemometer data

2000 ◽  
pp. 183
Author(s):  
Paolo Martano
Keyword(s):  
Roughness Length ◽  
Sonic Anemometer ◽  
Sensible Heat Flux ◽  
Proper Function ◽  
Data Sets ◽  
Direct Estimate ◽  
Data Set ◽  
Single Level ◽  
Level Data ◽  
Sonic Anemometer Data

The estimation of joint values of both the roughness length z0 and the displacement height d is considered in the context of the MoninObukhov similarity law for the windspeed profile. When focused on single level data sets from one sonic anemometer (i.e. wind velocity, Reynolds stress and sensible heat flux data sets at one height), it is shown that this problem can be reduced to a simpler least squares procedure for one variable only. This procedure is carried out over a proper function of the data, representing the relative uncertainty of the roughness length, σz0/z0. This is minimized with respect to d, giving a direct estimate of d, z0, and their statistical uncertainty. The scheme is tested against a field-experiment data set.

scholarly journals Induced fit with replica exchange improves protein complex structure prediction

2021 ◽  
Author(s):  
Ameya Harmalkar ◽  
Sai Pooja Mahajan ◽  
Jeffrey J. Gray
Keyword(s):  
Conformational Changes ◽  
Protein Complex ◽  
Structure Prediction ◽  
Protein Complexes ◽  
Complex Structure ◽  
Replica Exchange ◽  
Conformational Sampling ◽  
Success Rates ◽  
Induced Fit ◽  
Protein Size

Despite the progress in prediction of protein complexes over the last decade, recent blind protein complex structure prediction challenges revealed limited success rates (less than 20% models with DockQ score > 0.4) on targets that exhibit significant conformational change upon binding. To overcome limitations in capturing backbone motions, we developed a new, aggressive sampling method that incorporates temperature replica exchange Monte Carlo (T-REMC) and conformational sampling techniques within docking protocols in Rosetta. Our method, ReplicaDock 2.0, mimics induced-fit mechanism of protein binding to sample backbone motions across putative interface residues on-the-fly, thereby recapitulating binding-partner induced conformational changes. Furthermore, ReplicaDock 2.0 clocks in at 150-500 CPU hours per target (protein-size dependent); a runtime that is significantly faster than Molecular Dynamics based approaches. For a benchmark set of 88 proteins with moderate to high flexibility (unbound-to-bound iRMSD over 1.2 Angstroms), ReplicaDock 2.0 successfully docks 61% of moderately flexible complexes and 35% of highly flexible complexes. Additionally, we demonstrate that by biasing backbone sampling particularly towards residues comprising flexible loops or hinge domains, highly flexible targets can be predicted to under 2 angstrom accuracy. This indicates that additional gains are possible when mobile protein segments are known.

Rotational Characteristics of the Green Solar Corona: 1947-1991

1994 ◽  
Vol 144 ◽  
pp. 139-141 ◽  
Author(s):  
J. Rybák ◽  
V. Rušin ◽  
M. Rybanský
Keyword(s):  
Solar Corona ◽  
World Wide ◽  
Rotation Period ◽  
Original Data ◽  
Coronal Emission ◽  
Time Intervals ◽  
Data Set ◽  
The World ◽  
Coronal Emission Line ◽  
Homogeneous Data

AbstractFe XIV 530.3 nm coronal emission line observations have been used for the estimation of the green solar corona rotation. A homogeneous data set, created from measurements of the world-wide coronagraphic network, has been examined with a help of correlation analysis to reveal the averaged synodic rotation period as a function of latitude and time over the epoch from 1947 to 1991.The values of the synodic rotation period obtained for this epoch for the whole range of latitudes and a latitude band ±30° are 27.52±0.12 days and 26.95±0.21 days, resp. A differential rotation of green solar corona, with local period maxima around ±60° and minimum of the rotation period at the equator, was confirmed. No clear cyclic variation of the rotation has been found for examinated epoch but some monotonic trends for some time intervals are presented.A detailed investigation of the original data and their correlation functions has shown that an existence of sufficiently reliable tracers is not evident for the whole set of examinated data. This should be taken into account in future more precise estimations of the green corona rotation period.

Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

1982 ◽  
Vol 40 ◽  
pp. 74-75
Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser
Keyword(s):  
Purple Membrane ◽  
Data Set ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fourier Techniques ◽  
Versus Protein ◽  
The Difference ◽  
Difference Fourier ◽  
Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

Algorithms for automated montage synthesis of images from laser-scanning confocal microscopes

1995 ◽  
Vol 53 ◽  
pp. 650-651
Author(s):  
D. E. Becker
Keyword(s):  
Image Analysis ◽  
High Resolution ◽  
Laser Scanning ◽  
Cell Counting ◽  
Wide Area ◽  
Data Set ◽  
Computational Synthesis ◽  
Automated Cell Counting ◽  
Partial View ◽  
The Individual

An efficient, robust, and widely-applicable technique is presented for computational synthesis of high-resolution, wide-area images of a specimen from a series of overlapping partial views. This technique can also be used to combine the results of various forms of image analysis, such as segmentation, automated cell counting, deblurring, and neuron tracing, to generate representations that are equivalent to processing the large wide-area image, rather than the individual partial views. This can be a first step towards quantitation of the higher-level tissue architecture. The computational approach overcomes mechanical limitations, such as hysterisis and backlash, of microscope stages. It also automates a procedure that is currently done manually. One application is the high-resolution visualization and/or quantitation of large batches of specimens that are much wider than the field of view of the microscope.The automated montage synthesis begins by computing a concise set of landmark points for each partial view. The type of landmarks used can vary greatly depending on the images of interest. In many cases, image analysis performed on each data set can provide useful landmarks. Even when no such “natural” landmarks are available, image processing can often provide useful landmarks.

Merging of electron-diffraction intensities acquired with a slow-scan CCD camera of crotoxin complex crystals to 3.5Å resolution

1994 ◽  
Vol 52 ◽  
pp. 104-105
Author(s):  
Jaap Brink ◽  
Wah Chiu
Keyword(s):  
Electron Diffraction ◽  
Ccd Camera ◽  
Crystal Thickness ◽  
Local Contrast ◽  
Camera Model ◽  
Data Set ◽  
3 Dimensional ◽  
Diffraction Mode ◽  
Diffraction Patterns ◽  
Complex Crystals

Crotoxin complex is the principal neurotoxin of the South American rattlesnake, Crotalus durissus terrificus and has a molecular weight of 24 kDa. The protein is a heterodimer with subunit A assigneda chaperone function. Subunit B carries the lethal activity, which is exerted on both sides ofthe neuro-muscular junction, and which is thought to involve binding to the acetylcholine receptor. Insight in crotoxin complex’ mode of action can be gained from a 3 Å resolution structure obtained by electron crystallography. This abstract communicates our progress in merging the electron diffraction amplitudes into a 3-dimensional (3D) intensity data set close to completion. Since the thickness of crotoxin complex crystals varies from one crystal to the other, we chose to collect tilt series of electron diffraction patterns after determining their thickness. Furthermore, by making use of the symmetry present in these tilt data, intensities collected only from similar crystals will be merged.Suitable crystals of glucose-embedded crotoxin complex were searched for in the defocussed diffraction mode with the goniometer tilted to 55° of higher in a JEOL4000 electron cryo-microscopc operated at 400 kV with the crystals kept at -120°C in a Gatan 626 cryo-holder. The crystal thickness was measured using the local contrast of the crystal relative to the supporting film from search-mode images acquired using a 1024 x 1024 slow-scan CCD camera (model 679, Gatan Inc.).

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