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moreira irina s. (curatore); machuqueiro miguel (curatore); mourão joana (curatore) - computational design of membrane proteins

Computational Design of Membrane Proteins

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Dettagli

Genere:Libro
Lingua: Inglese
Editore:

Humana

Pubblicazione: 07/2022
Edizione: 1st ed. 2021





Trama

This volume provides an overview of the current successes as well as pitfalls and caveats that are hindering the design of membrane proteins. Divided into six parts, chapters detail membrane transporter, FoldX force field, protein stability, G-Protein Coupled Receptors (GPCR) structures, transmembrane helices, membrane molecular dynamics (MD) simulations, pH-dependent protonation states, membrane permeability, and passive transport. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge,  Computational Design of Membrane Proteins aims to ensure successful results in the further study of this vital field.

Chapter 4 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.









Sommario

PART I: INTRODUCTION

1          Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View

            Nícia Rosário-Ferreira, Catarina Marques-Pereira, Raquel P. Gouveia, Joana Mourão, and Irina S. Moreira

 

PART II          METHODS IN SYNTHETIC BIOLOGY

 

2          Integrating Membrane Transporter Proteins into Droplet Interface Bilayers

            Heather E. Findlay, Nicola J. Harris, and Paula J. Booth

 

3          Membrane Protein Engineering with Rosetta

            Rebecca F. Alford and Jeffrey J. Gray

 

4          Engineering of Biological Pathways: Complex Formation and Signal Transduction

            Philipp Junk and Christina Kiel

 

PART III        STRUCTURE PREDICTION AND OLIGOMERIZATION

 

5          Homology Modeling of Class a G-protein-coupled Receptors in the Age of the Structure Boom

Asma Tiss, Rym Ben Boubaker, Daniel Henrion, Hajer Guissouma, and Marie Chabbert

 

6          Interface Prediction for GPCR Oligomerization between Transmembrane Helices

            Wataru Nemoto and Akira Saito

 

7          Memdock: An a-Helical Membrane Protein Docking Algorithm

            Naama Hurwitz and Haim J. Wolfson

 

PART IV        COARSE-GRAINED AND ATOMISTIC MD SIMULATIONS

 

8          Identification and Characterization of specific Protein-Lipid Interactions using       Molecular Simulation

            Robin A. Corey, Mark S. P. Sansom, and Phillip J. Stansfeld

 

9          Molecular Dynamics Simulation of Lipid-modified Signaling Proteins

            Vinay Nair and Alemayehu A. Gorfe

 

10        In silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides

            Nicolas Frazee, Violeta Burns, Chitrak Gupta, and Blake Mertz

 

PART V          PH AND POLARIZATION EFFECTS

 

11        pKa Calculations in Membrane Proteins from Molecular Dynamics Simulations

            Nuno F. B. Oliveira, Tomás F. D. Silva, Pedro B. P. S. Reis, and Miguel Machuqueiro

 

12        Poor person’s pH Simulation of Membrane Proteins

            Chitrak Gupta, Umesh Khaniya, John W. Vant, Mrinal Shekhar, Junjun Mao, M. R. Gunner, and Abhishek Singharoy

13        Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model

            Justin Lemkul

 

PART VI        MEMBRANE PERMEABILITY AND TRANSPORT

 

14        In silico Prediction of Permeability Coefficients

Ricardo J. Ferreira

 

15        Identification of Pan Assay INterference compoundS (PAINS) using an MD-Based Protocol

Pedro R. Magalhães, Pedro B. P. S. Reis, Diogo Vila-Viçosa, Miguel Machuqueiro, and Bruno Victor

 

16        Transmembrane Anion Transport Mediated by Halogen Bonds: using Off-Center Charges

            Paulo J. Costa











Altre Informazioni

ISBN:

9781071614709

Condizione: Nuovo
Collana: Methods in Molecular Biology
Dimensioni: 254 x 178 mm Ø 581 gr
Formato: Brossura
Illustration Notes:XI, 290 p. 57 illus., 53 illus. in color.
Pagine Arabe: 290
Pagine Romane: xi


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