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Minicollagen cysteine-rich domains encode distinct modes of polymerization to form stable nematocyst capsules

Abstract

Not specified

Authors: Anja Tursch, Davide Mercadante, Jutta Tennigkeit, Frauke Gräter, Suat Özbek

Date Published: 2016

Publication Type: Journal

Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control

Abstract

Not specified

Authors: Lisa M Kent, Trevor S Loo, Laurence D Melton, Davide Mercadante, Martin AK Williams, Geoffrey B Jameson

Date Published: 2016

Publication Type: Journal

Human DPP III – Keap1 Interactions: A Combined Experimental And Computational study

Abstract

Not specified

Authors: Mario Gundić, Antonija Tomić, Rebecca C. Wade, Mihaela Matovina, Zrinka Karačić, Saša Kazazić, Sanja Tomić

Date Published: 2016

Publication Type: Journal

Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets

Abstract

Not specified

Authors: Daria B. Kokh, Paul Czodrowski, Friedrich Rippmann, Rebecca C. Wade

Date Published: 2016

Publication Type: Journal

Three steps to Gold: Mechanism of protein adsorption to a gold surface revealed by Brownian and molecular dynamics simulations

Abstract

Not specified

Authors: M. Ozboyaci, D. B. Kokh, R. C. Wade

Date Published: 2016

Publication Type: Journal

Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer

Abstract

Not specified

Authors: Xiaofeng Yu, Daria B. Kokh, Prajwal Nandekar, Ghulam Mustafa, Stefan Richter, Rebecca C. Wade

Date Published: 2016

Publication Type: InCollection

Modeling and simulation of protein–surface interactions: achievements and challenges

Abstract (Expand)

Understanding protein–inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of … experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein–surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein–surface interactions and discuss the successes and limitations of current approaches.

Authors: Musa Ozboyaci, Daria B. Kokh, Stefano Corni, Rebecca C. Wade

Date Published: 2016

Publication Type: Journal

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