Hydrogen Bonds and Kinematic Mobility of Protein Molecules

2010 ◽  
Vol 2 (2) ◽  
Author(s):  
Zahra Shahbazi ◽  
Horea T. Ilieş ◽  
Kazem Kazerounian
Keyword(s):  
Hydrogen Bonds ◽  
Degrees Of Freedom ◽  
Point Of View ◽  
Folding Process ◽  
Kinematic Chains ◽  
Protein Molecules ◽  
Internal Mobility ◽  
Lower Mobility ◽  
Folding Simulations ◽  
And Function

Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation, and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOFs) with considerable computational implications. On the other hand, real protein molecules appear to exhibit a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of hydrogen bonds during the folding process. In this paper, we explore the pivotal role of hydrogen bonds in determining the structure and function of the proteins from the point of view of mechanical mobility. The existing geometric criteria on the formation of hydrogen bonds are reviewed and a new set of geometric criteria is proposed. We show that the new criteria better correlate the number of predicted hydrogen bonds with those established by biological principles than other existing criteria. Furthermore, we employ established tools in kinematics mobility analysis to evaluate the internal mobility of protein molecules and to identify the rigid and flexible segments of the proteins. Our results show that the developed procedure significantly reduces the DOF of the protein models, with an average reduction of 94%. Such a dramatic reduction in the number of DOF can have enormous computational implications in protein folding simulations.

On Hydrogen Bonds and Mobility of Protein Molecules

2009 ◽  
Author(s):  
Zahra Shahbazi ◽  
Horea T. Ilies¸ ◽  
Kazem Kazerounian
Keyword(s):  
Hydrogen Bonds ◽  
Degrees Of Freedom ◽  
Point Of View ◽  
Folding Process ◽  
Kinematic Chains ◽  
Protein Molecules ◽  
Internal Mobility ◽  
Lower Mobility ◽  
Folding Simulations ◽  
And Function

Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOF) with considerable computational implications. On the other hand, real protein molecules appear to exhibits a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of Hydrogen bonds during the folding process. In this paper we explore the pivotal role of Hydrogen bonds in determining the structure and function of the proteins from the point of view of mechanical mobility. The existing geometric criteria on the formation of Hydrogen bonds are reviewed and a new set of geometric criteria are proposed. We show that the new criteria better correlate the number of predicted Hydrogen bonds with those established by biological principles than other existing criteria. Furthermore, we employ established tools in kinematics mobility analysis to evaluate the internal mobility of protein molecules, and to identify the rigid and flexible segments of the proteins. Our results show that the developed procedure significantly reduces the DOF of the protein models, with an average reduction of 94%. Such a dramatic reduction in the number of DOF can have has enormous computational implications in protein folding simulations.

Protein Molecules as Natural Nano Bio Devices: Mobility Analysis

2010 ◽  
Author(s):  
Zahra Shahbazi ◽  
Horea T. Ilies¸ ◽  
Kazem Kazerounian
Keyword(s):  
Degrees Of Freedom ◽  
Conformational Transitions ◽  
Living Cells ◽  
Mobility Analysis ◽  
Folding Process ◽  
Kinematic Chains ◽  
Protein Molecules ◽  
Kinematic Models ◽  
Lower Mobility ◽  
Molecular Components

Proteins are nature’s nano-robots in the form of functional molecular components of living cells. The function of these natural nano-robots often requires conformational transitions between two or more native conformations that are made possible by the intrinsic mobility of the proteins. Understanding these transitions is essential to the understanding of how proteins function, as well as to the ability to design and manipulate protein-based nano-mechanical systems [1]. Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOF) with considerable computational implications. On the other hand, real protein molecules appear to exhibits a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of Hydrogen bonds during the folding process.

Kinematic Motion Constraints of the Protein Molecule Chains

2011 ◽  
Author(s):  
Zahra Shahbazi ◽  
Horea T. Ilies¸ ◽  
Kazem Kazerounian
Keyword(s):  
Hydrogen Bonds ◽  
Degrees Of Freedom ◽  
Main Chain ◽  
Protein Structures ◽  
Protein Molecule ◽  
Correct Identification ◽  
Closed Loops ◽  
Motion Constraints ◽  
Protein Molecules ◽  
Internal Mobility

The function of protein molecules is defined by their 3-D geometry, as well as their internal mobility, which is heavily influenced by the internal hydrogen bonds. The correct identification of these hydrogen bonds and the prediction of their effect on the mobility of protein molecules can provide an invaluable mechanism to understand protein behavior. Applications of this study ranges from nano-engineering to new drug design. We are extending our recent approach from identifying main-chain main-chain hydrogen bonds to all types of hydrogen bonds that occur in protein structures, such as α-helices and β-sheets. We use the Gru¨bler-Kutzbach kinematic mobility criterion to determine the degrees of freedom of all closed loops (rigid loops as well as closed loops of one or more degrees of freedom) formed by Hydrogen bonds. Furthermore, we systematically develop constraint equations for non-rigid closed loops. Several examples of protein molecules from PDB are used to show that these additions both improve the accuracy of mobility analysis and enable us to study a broader range of the motion of protein molecules. This approach offers theoretical insight as well as extensive numerical efficiencies in protein simulations.

scholarly journals Exoskeleton kinematic design robustness: An assessment method to account for human variability

2020 ◽  
Vol 1 ◽  
Author(s):  
Matteo Sposito ◽  
Christian Di Natali ◽  
Stefano Toxiri ◽  
Darwin G. Caldwell ◽  
Elena De Momi ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Pilot Trial ◽  
Kinematic Model ◽  
Assessment Method ◽  
Point Of View ◽  
Systematic Method ◽  
Kinematic Chains ◽  
Subject Variability ◽  
Anchor Points ◽  
Human Joints

Abstract Exoskeletons are wearable devices intended to physically assist one or multiple human joints in executing certain activities. From a mechanical point of view, they are kinematic structures arranged in parallel to the biological joints. In order to allow the users to move while assisted, it is crucial to avoid mobility restrictions introduced by the exoskeleton’s kinematics. Passive degrees of freedom and other self-alignment mechanisms are a common option to avoid any restrictions. However, the literature lacks a systematic method to account for large inter- and intra-subject variability in designing and assessing kinematic chains. To this end, we introduce a model-based method to assess the kinematics of exoskeletons by representing restrictions in mobility as disturbances and undesired forces at the anchor points. The method makes use of robotic kinematic tools and generates useful insights to support the design process. Though an application on a back-support exoskeleton designed for lifting tasks is illustrated, the method can describe any type of rigid exoskeleton. A qualitative pilot trial is conducted to assess the kinematic model that proved to predict kinematic configurations associated to rising undesired forces recorded at the anchor points, that give rise to mobility restrictions and discomfort on the users.

Real-Time Direct Position Analysis of Parallel Spherical Wrists by Using Extra Sensor Data

2004 ◽  
Author(s):  
R. Vertechy ◽  
V. Parenti-Castelli
Keyword(s):  
Real Time ◽  
Measurement Errors ◽  
Degrees Of Freedom ◽  
Point Of View ◽  
The Body ◽  
Least Square ◽  
Sensor Data ◽  
End Effector ◽  
Kinematic Chains ◽  
Position Analysis

The paper presents an algorithm for the real-time evaluation of the actual end-effector orientation (pose) of general parallel spherical wrists. Conceptually, the method relies on the evidence that the pose of a rigid body is defined once the location of at least two linearly independent vectors attached to the body is known. The location of these vectors of the wrist end-effector is determined by the solution of the direct position analysis of some properly chosen kinematic chains (legs) of the manipulator. In order to accomplish this analysis, extra-sensors, which measure suitable non-actuated variables of the chosen legs, need to be placed in addition to the ones normally embedded in the servo motors, i.e. the sensors which measure the actuated variables. From a mathematical point of view, the algorithm is built on the Polar Decomposition of a matrix and has inherent least square features. Thus, together with measurement redundancy, i.e. more sensors (extra-sensors) than the mechanism degrees of freedom, the method also allows minimizing the influence of both round-off and measurement errors on the estimation of the location of the wrist end-effector. The method is general but, in order to prove its effectiveness, without loss of generality it has been customized to the solution of the (3-UPS)S fully parallel wrist architecture. Comparison of the proposed method, in both its general and specialized form, with others from the literature is provided.

An Optimized Kinematic Mobility Analysis of Protein Molecules

2014 ◽  
Author(s):  
Ahmet Demirtas ◽  
Zahra Shahbazi
Keyword(s):  
Degrees Of Freedom ◽  
3D Structure ◽  
Computational Cost ◽  
Random Group ◽  
Kinematic Chains ◽  
Simulation Speed ◽  
Modified Method ◽  
Rigidity Analysis ◽  
Protein Molecules ◽  
Pebble Game

Understanding the 3D structure and consequently the motion of protein molecules contributes to simulate their function. Modeling protein molecules as kinematic chains has been used to predict protein molecules flexible and rigid regions as well as their degrees of freedom to predict their mobility. However, high computational cost for relatively large molecules is one of the major challenges in this field. In this paper we have combined our previously developed rigidity analysis (ProtoFold) with pebble game thus improving computational cost of our simulation. Here, we have determined the required time for all steps of ProtoFold and subsequently the most time consuming step. Results have shown that finding rigid loops inside the protein structure using graph theory and Grübler-Kutzbach criterion is the slowest part of the procedure, taking an average of 75% of the time required for the rigidity analysis. Therefore we have replaced this step with pebble game. The modified method has been applied to a random group of protein molecules and its efficiency in significantly improving the simulation speed has been verified.

Real-Time Direct Position Analysis of Parallel Spherical Wrists by Using Extra Sensors

2005 ◽  
Vol 128 (1) ◽  
pp. 288-294 ◽  
Author(s):  
R. Vertechy ◽  
V. Parenti-Castelli
Keyword(s):  
Real Time ◽  
Measurement Errors ◽  
Degrees Of Freedom ◽  
Point Of View ◽  
The Body ◽  
Least Square ◽  
End Effector ◽  
Kinematic Chains ◽  
Position Analysis ◽  
Specialized Form

The paper presents an algorithm for the real-time evaluation of the actual end-effector orientation of general parallel spherical wrists. Conceptually, the method relies on evidence that the pose of a rigid body is defined once the location of at least two linearly independent vectors attached to the body is known. The location of these vectors of the wrist end-effector is determined by the solution of the direct position analysis of some properly chosen kinematic chains (legs) of the manipulator. In order to accomplish this analysis, extra sensors, which measure suitable non-actuated variables of the chosen legs, need to be placed in addition to the ones normally embedded in the servomotors, i.e., the sensors which measure the actuated variables. From a mathematical point of view, the algorithm is built on the polar decomposition of a matrix and has inherent least square features. Thus, together with measurement redundancy, i.e., more sensors (extra sensors) than the mechanism degrees of freedom, the method also makes it possible to minimize the influence of both round-off and measurement errors on the estimation of the location of the wrist end-effector. The method is general but, in order to prove its effectiveness, without loss of generality it has been customized to the solution of the 3(UPS)-S fully parallel wrist architecture (where U, P and S are for universal, prismatic and spherical joint, respectively). Comparison of the proposed method, in both its general and specialized form, with others from the literature is provided.

scholarly journals Organotin(IV) selenate derivatives – Crystal structure of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n

2021 ◽  
Vol 44 (1) ◽  
pp. 213-217
Author(s):  
Waly Diallo ◽  
Hélène Cattey ◽  
Laurent Plasseraud
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Point Of View ◽  
Intermolecular Hydrogen Bonds

Abstract Crystallization of [(Ph3Sn)2SeO4] ⋅ 1.5H2O in methanol leads to the formation of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n (1) which constitutes a new specimen of organotin(IV) selenate derivatives. In the solid state, complex 1 is arranged in polymeric zig-zag chains, composed of alternating Ph3Sn and SeO4 groups. In addition, pendant Ph3Sn ⋅ CH3OH moieties are branched along chains according to a syndiotactic organization and via Sn-O-Se connections. From a supramolecular point of view, intermolecular hydrogen bonds established between the selenate groups (uncoordinated oxygen) and the hydroxyl functions (CH3OH) of the pendant groups link the chains together.

scholarly journals Expression and Function of Organic Anion Transporting Polypeptides in the Human Brain: Physiological and Pharmacological Implications

Pharmaceutics ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 834
Author(s):  
Anima M. Schäfer ◽  
Henriette E. Meyer zu Schwabedissen ◽  
Markus Grube
Keyword(s):  
Organic Anion ◽  
Physiological Role ◽  
Point Of View ◽  
Efflux Transporters ◽  
Organic Anion Transporting Polypeptides ◽  
Current State ◽  
P Glycoprotein ◽  
The Central Nervous System ◽  
And Function ◽  
Uptake Transporters

The central nervous system (CNS) is an important pharmacological target, but it is very effectively protected by the blood–brain barrier (BBB), thereby impairing the efficacy of many potential active compounds as they are unable to cross this barrier. Among others, membranous efflux transporters like P-Glycoprotein are involved in the integrity of this barrier. In addition to these, however, uptake transporters have also been found to selectively uptake certain compounds into the CNS. These transporters are localized in the BBB as well as in neurons or in the choroid plexus. Among them, from a pharmacological point of view, representatives of the organic anion transporting polypeptides (OATPs) are of particular interest, as they mediate the cellular entry of a variety of different pharmaceutical compounds. Thus, OATPs in the BBB potentially offer the possibility of CNS targeting approaches. For these purposes, a profound understanding of the expression and localization of these transporters is crucial. This review therefore summarizes the current state of knowledge of the expression and localization of OATPs in the CNS, gives an overview of their possible physiological role, and outlines their possible pharmacological relevance using selected examples.

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