Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations
نویسندگان
چکیده
منابع مشابه
Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations
Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the m...
متن کاملMolecular dynamics simulations of atomic-level brittle fracture mechanisms in amorphous silica
We have examined the atomic dynamics of the brittle fracture process in amorphous silica using molecular dynamics. Under strain, extensive atomic restructuring occur in the vicinity of voids leading to the formation of 2membered (2-M) silica rings that are much different than the open network structure of the bulk. The sequence of events that lead to the formation of the 2-M rings was character...
متن کاملProtein Allostery and Conformational Dynamics.
The functions of many proteins are regulated through allostery, whereby effector binding at a distal site changes the functional activity (e.g., substrate binding affinity or catalytic efficiency) at the active site. Most allosteric studies have focused on thermodynamic properties, in particular, substrate binding affinity. Changes in substrate binding affinity by allosteric effectors have gene...
متن کاملDesigning a new tetrapeptide to inhibit the BIR3 domain of the XIAP protein via molecular dynamics simulations
The XIAP protein is a member of apoptosis proteins family. The XIAP protein plays a central role in the inhibition of apoptosis and consists of three Baculoviral IAP Repeat domains. The BIR3 domain binds directly to the N-terminal of caspase-9 and therefore it inhibits apoptosis. N-terminal tetrapeptide region of SMAC protein can bind to BIR3, inhibit it and subsequently induce apoptosis. In th...
متن کاملAtomic/Molecular-Level Simulations of Laser–Materials Interactions
Molecular/atomic-level computer modeling of laser–materials interactions is playing an increasingly important role in the investigation of complex and highly nonequilibrium processes involved in short-pulse laser processing and surface modification. This chapter provides an overview of recent progress in the development of computational methods for simulation of laser interactions with organic ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: PLOS Computational Biology
سال: 2016
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.1004746