Extension of the Kinematics-Based Method for Predicting the Motion of Proteins

2014 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Computational Cost ◽  
Three Dimensional ◽  
Structural Data ◽  
Data Bank ◽  
Serial Manipulators ◽  
Protein Model ◽  
The Matrix ◽  
Basic Equations ◽  
Definition Of ◽  
Structural Compliance

On the basis of an analogy between the kinematic structures of proteins and robotic mechanisms, we have so far developed methods for predicting the internal motion of proteins from three-dimensional structural data in the protein data bank (PDB). With these methods, we model proteins as serial manipulators constrained by springs, and calculate the structural compliance of the protein model. In this study, toward more practical purposes, we reformulate and extend the existing methods by broadening the definition of structural compliance and reducing the number of variables for expressing the conformation of the model. The broadening is performed by separating the parts whose deformations are evaluated from those where forces are applied. This separation allows the calculation of the effective forces causing deformation in other specified parts. We also reduce the number of conformation variables from the consideration based on the algebraic structure of the basic equations. The size of the matrix whose inverse must be calculated is thus minimized, and the computational cost is reduced. We verify the effectiveness of these extensions by analyzing the PDB data of some proteins.

Analyzing Motion Properties of Proteins Affected by Localized Structures From a Robot Kinematics Perspective

2015 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Protein Data Bank ◽  
Complex Shape ◽  
Structural Data ◽  
Data Bank ◽  
Robot Kinematics ◽  
Motion Prediction ◽  
Serial Manipulators ◽  
Localized Structures ◽  
Motion Modes ◽  
Structural Compliance

On the basis of robot kinematics, we have thus far developed a method for predicting the motion of proteins from their 3D structural data given in the Protein Data Bank (PDB data). In this method, proteins are modeled as serial manipulators constrained by springs and the structural compliance properties of the models are evaluated. We focus on localized instead of whole structures of proteins. Employing the same model used in our method of motion prediction, the motion properties of the localized structures and the relation between the motion properties of localized and whole structures are analyzed. First, we present a method for graphically expressing the deformation of objects with a complex shape, such as proteins, by approximating the shape as a rectangular prism with a mesh on its surface. We then formulate a method for comparing the motion properties of localized structures cleaved from the whole structure and those remaining in it by expressing the motion of the latter using the decomposed motion modes of the former according to the structural compliance. Finally, we show a method for evaluating the effect of a localized structure on the motion properties of proteins by applying forces to localized structures. In the formulations, we demonstrate applications as illustrative examples using the PDB data of a real protein.

Structural Compliance Analysis and Internal Motion Properties of Proteins From a Robot Kinematics Perspective: Formulation of Basic Equations

2016 ◽  
Vol 8 (2) ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Kinematic Model ◽  
Structural Data ◽  
Forced Response ◽  
Internal Motion ◽  
Robot Kinematics ◽  
Dihedral Angles ◽  
Protein Model ◽  
Applied Forces ◽  
Basic Equations ◽  
Structural Compliance

From a perspective of robot kinematics, we develop a method for predicting internal motion properties and understanding the functions of proteins from their three-dimensional (3D) structural data (protein data bank (PDB) data). The key ideas are based on the structural compliance analysis of proteins. In this paper, we mainly discuss the basic equations for the analysis. First, a kinematic model of a protein is introduced. Proteins are simply modeled as serial manipulators constrained by linear springs, where the dihedral angles on the main chains correspond to the joint angles of manipulators. Then, the kinematic equations of the protein model are derived. In particular, the forced response or the deformation caused by the forces in static equilibrium forms the basis for the structural compliance analysis. In the formulations, the protein models are regarded as manipulators that control the positions in the model or the distances between them, by the dihedral angles on the main chains. Next, the structural compliance of the protein model is defined, and a method for extracting the information about the internal motion properties from the structural compliance is shown. In general, the structural compliance refers to the relationship between the applied forces and the deformation of the parts surrounded by the application points. We define it in a more general form by separating the parts whose deformations are evaluated from those where forces are applied. When decomposing motion according to the magnitude of the structural compliance, we can infer that the lower compliance motion will easily occur. Finally, we show two application examples using PDB data of lactoferrin and hemoglobin. Despite using an approximate protein model, the predicted internal motion properties agree with the measured ones.

Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses

2016 ◽  
Vol 72 (3) ◽  
pp. 324-337 ◽  
Author(s):  
A. Janner
Keyword(s):  
Lattice Point ◽  
Three Dimensional ◽  
Structural Data ◽  
Data Bank ◽  
Coarse Grained ◽  
Large Set ◽  
Fine Grained ◽  
Coarse Grained Model ◽  
Digital Modeling ◽  
Icosahedral Viruses

Considered is the coarse-grained modeling of icosahedral viruses in terms of a three-dimensional lattice (the digital modeling lattice) selected among the projected points in space of a six-dimensional icosahedral lattice. Backbone atomic positions (Cα's for the residues of the capsid and phosphorus atoms P for the genome nucleotides) are then indexed by their nearest lattice point. This leads to a fine-grained lattice point characterization of the full viral chains in the backbone approximation (denoted as digital modeling). Coarse-grained models then follow by a proper selection of the indexed backbone positions, where for each chain one can choose the desired coarseness. This approach is applied to three viruses, the Satellite tobacco mosaic virus, the bacteriophage MS2 and the Pariacoto virus, on the basis of structural data from the Brookhaven Protein Data Bank. In each case the various stages of the procedure are illustrated for a given coarse-grained model and the corresponding indexed positions are listed. Alternative coarse-grained models have been derived and compared. Comments on related results and approaches, found among the very large set of publications in this field, conclude this article.

A generalized Archie’s law for n phases

Geophysics ◽  
2010 ◽  
Vol 75 (6) ◽  
pp. E247-E265 ◽  
Author(s):  
Paul W. J. Glover
Keyword(s):  
Volume Fraction ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Reservoir Rock ◽  
Archie’S Law ◽  
Phase Volume Fraction ◽  
General Law ◽  
Special Cases ◽  
The Matrix ◽  
Definition Of

Archie’s law has been the standard method for relating the conductivity of a clean reservoir rock to its porosity and the conductivity of its pore fluid for more than [Formula: see text]. However, it is applicable only when the matrix is nonconducting. A modified version that allows a conductive matrix was published in 2000. A generalized form of Archie’s law is studied for any number of phases for which the classical Archie’s law and modified Archie’s law for two phases are special cases. The generalized Archie’s law contains a phase conductivity, a phase volume fraction, and phase exponent for each of its [Formula: see text] phases. The connectedness of each of the phases is considered, and the principle of conservation of connectedness in a three-dimensional multiphase mixture is introduced. It is confirmed that the general law is formally the same as the classical Archie’s law and modified Archie’s law for one and two conducting phases, respectively. The classical second Archie’s law is compared with the generalized law, which leads to the definition of a saturation exponent for each phase. This process has enabled the derivation of relationships between the phase exponents and saturation exponents for each phase. The relationship between percolation theory and the generalized model is also considered. The generalized law is examined in detail for two and three phases and semiquantitatively for four phases. Unfortunately, the law in its most general form is very difficult to prove experimentally. Instead, numerical modeling in three dimensions is carried out to demonstrate that it behaves well for a system consisting of four interacting conducting phases.

scholarly journals Relevant aspects to the recognition of extensional environments in the field

2021 ◽  
Vol 48 (2) ◽  
pp. 95-106
Author(s):  
Ana Milena Suárez Arias ◽  
Julián Andrés López Isaza ◽  
Anny Juieth Forero Ortega ◽  
Mario Andrés Cuéllar Cárdenas ◽  
Carlos Augusto Quiroz Prada ◽  
...  
Keyword(s):  
Hanging Wall ◽  
Image Interpretation ◽  
Three Dimensional ◽  
Normal Fault ◽  
Structural Data ◽  
Structural Aspect ◽  
Half Graben ◽  
Regional Tectonic ◽  
History Of ◽  
Definition Of

The understanding of each geological-structural aspect in the field is fundamental to be able to reconstruct the geological history of a region and to give a geological meaning to the data acquired in the outcrop. The description of a brittle extensional environment, which is dominated by normal fault systems, is based on: (I)  image interpretation, which aims to find evidence suggestive of an extensional geological environment, such  as the presence of scarp lines and fault scarps, horst, graben and/or half-graben, among others, that allow the identification of the footwall and hanging wall blocks; ii) definition of the sites of interest for testing; and  iii) analysis of the outcrops, following a systematic procedure that consists of the observation and identification of the deformation markers, their three-dimensional schematic representation, and their  subsequent interpretation, including the stereographic representation in the outcrop. This procedure implies the unification of the parameters of structural data acquisition in the field, mentioning the minimum fields  necessary for the registration of the data in tables. Additionally, the integration of geological and structural observations of the outcrop allows to understand the nature of the geological units, the deformation related to the extensional environment and the regional tectonic context of the study area.

A Computational Framework for Predicting the Motions of a Protein System From a Robot Kinematics Viewpoint

2013 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Robot Manipulator ◽  
Structural Data ◽  
Protein Molecule ◽  
Data Bank ◽  
Computational Time ◽  
Robot Kinematics ◽  
Efficient Computation ◽  
Elastic Network Model ◽  
Computational Framework ◽  
Structural Compliance

There is an analogy between the kinematic structures of proteins and robotic mechanisms. On the basis of this analogy, we have so far developed some methods for predicting the internal motions of proteins from their three-dimensional structural data in protein data bank (PDB). However, these methods are basically applicable to a single protein molecule. In this study, we extended these methods to apply them to systems that consist of multiple molecules including proteins (protein systems), and developed a computational framework for predicting the motions of the molecules. The model used in this method is a type of elastic network model. In particular, proteins are modeled as a robot manipulator constrained by the springs (the dihedral angles on the main chains correspond to the joint angles). The interactions between molecules are also modeled as springs. The basic concept for predicting the motions is based on the analysis of structural compliance. By applying statically balanced forces to the model in various directions, we extracted those motions with larger structural compliance. To reduce the computational time, we formulated the method with the prospect of efficient computation including parallel computation. In addition, we developed a preparatory computer program implementing the proposed algorithms, and analyzed some protein systems. The results showed that the proposed computational framework can efficiently analyze large protein systems.

scholarly journals AlphaFold-Predicted Structures of KCTD Proteins Unravel Previously Undetected Relationships among the Members of the Family

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1862
Author(s):  
Luciana Esposito ◽  
Nicole Balasco ◽  
Giovanni Smaldone ◽  
Rita Berisio ◽  
Alessia Ruggiero ◽  
...  
Keyword(s):  
Structural Information ◽  
Three Dimensional ◽  
Structural Data ◽  
Protein Family ◽  
General Sequence ◽  
Btb Domain ◽  
The Family ◽  
Three Dimensional Models ◽  
Definition Of ◽  
Sequence Similarities

One of the most striking features of KCTD proteins is their involvement in apparently unrelated yet fundamental physio-pathological processes. Unfortunately, comprehensive structure–function relationships for this protein family have been hampered by the scarcity of the structural data available. This scenario is rapidly changing due to the release of the protein three-dimensional models predicted by AlphaFold (AF). Here, we exploited the structural information contained in the AF database to gain insights into the relationships among the members of the KCTD family with the aim of facilitating the definition of the structural and molecular basis of key roles that these proteins play in many biological processes. The most important finding that emerged from this investigation is the discovery that, in addition to the BTB domain, the vast majority of these proteins also share a structurally similar domain in the C-terminal region despite the absence of general sequence similarities detectable in this region. Using this domain as reference, we generated a novel and comprehensive structure-based pseudo-phylogenetic tree that unraveled previously undetected similarities among the protein family. In particular, we generated a new clustering of the KCTD proteins that will represent a solid ground for interpreting their many functions.

Analyzing Internal Motion of Proteins From Viewpoint of Robot Kinematics: Formulation of Group Forced Response Method

2012 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Protein Structures ◽  
Computational Cost ◽  
Three Dimensional ◽  
Structural Data ◽  
Simple Calculation ◽  
Forced Response ◽  
Internal Motion ◽  
Robot Kinematics ◽  
Internal Motions ◽  
Applied Forces

An analogous relationship exists between the kinematic structures of proteins and robotic mechanisms. Hence, using this analogy, we attempt to understand the internal motions of proteins from the perspective of robot kinematics. In this study, we propose a method called group forced response (GFR) method for predicting the internal motion of proteins on the basis of their three-dimensional structural data (PDB data). In this method, we apply forces in static equilibrium to groups of atoms (e.g., secondary structures, domains, and subunits) and not to specific atoms. Furthermore, we predict the internal motion of proteins by analyzing the relative motion caused among groups by the applied forces. First, we show a method for approximately modeling protein structures as a robotic mechanism and the basic kinematic equations of the model. Next, the GFR method is formulated (e.g., Jacobian matrix for group motions, magnitude of forces applied to groups, and decomposition of motions into modes according to structural compliances). Finally, we present example applications of the proposed method in real protein structures. Despite the approximations in the model, low computational cost, and use of simple calculation parameters, the results almost agree with measured internal motions.

6-DOF Loading System with the Simulated Border

2012 ◽  
Vol 549 ◽  
pp. 894-898
Author(s):  
Bing Li ◽  
Yu Lan Wei ◽  
Yue Zhan Wang ◽  
Qi Bo Yan
Keyword(s):  
Degrees Of Freedom ◽  
Three Dimensional ◽  
Direction Cosine ◽  
Dimensional Structure ◽  
Structure Model ◽  
Technical Performance ◽  
Loading System ◽  
The Matrix ◽  
Definition Of ◽  
6 Degrees Of Freedom

There is a set of 6 degrees of freedom (6-DOF) loading system with the simulated border for the application of material structural strength and reliability tests. This is a novel equipment for the tests of structural mechanical properties and reliability in different materials. This study showed a three-dimensional structure model, introduced the definition of the test of the 6-DOF loading system with the simulated border, and discussed the primary theory of the system and technical performance. Based on the matrix of direction cosine of the system, the solutions of inverse kinematics of 6-DOF loading system were given. The system of control was introduced as well.

Application of high-resolution field-emission LVSEM, backscatter imaging, immunogold staining to definition of the spatial distributions of two human neutrophil adherence receptors

1993 ◽  
Vol 51 ◽  
pp. 36-37
Author(s):  
Robert D. Nelson ◽  
Sharon R. Hasslen ◽  
Stanley L. Erlandsen
Keyword(s):  
Cell Surface ◽  
Surface Membrane ◽  
Three Dimensional ◽  
Human Neutrophils ◽  
Spatial Distributions ◽  
Immunogold Staining ◽  
Functional Control ◽  
Neutrophil Adherence ◽  
Definition Of ◽  
Mode Of Attachment

Receptors are commonly defined in terms of number per cell, affinity for ligand, chemical structure, mode of attachment to the cell surface, and mechanism of signal transduction. We propose to show that knowledge of spatial distribution of receptors on the cell surface can provide additional clues to their function and components of functional control.L-selectin and Mac-1 denote two receptor populations on the neutrophil surface that mediate neutrophil-endothelial cell adherence interactions and provide for targeting of neutrophil recruitment to sites of inflammation. We have studied the spatial distributions of these receptors using LVSEM and backscatter imaging of isolated human neutrophils stained with mouse anti-receptor (primary) antibody and goat anti-mouse (secondary) antibody conjugated to 12 nm colloidal gold. This combination of techniques provides for three-dimensional analysis of the expression of these receptors on different surface membrane domains of the neutrophil: the ruffles and microvilli that project from the cell surface, and the cell body between these projecting structures.

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