scholarly journals Computational Analysis of HIV-1 Protease Protein Binding Pockets

2010 ◽  
Vol 50 (10) ◽  
pp. 1759-1771 ◽  
Author(s):  
Gene M. Ko ◽  
A. Srinivas Reddy ◽  
Sunil Kumar ◽  
Barbara A. Bailey ◽  
Rajni Garg
Keyword(s):  
Protein Binding ◽  
Computational Analysis ◽  
Binding Pockets ◽  
Hiv 1

scholarly journals Novel computational analysis of protein binding array data identifies direct targets of Nkx2.2 in the pancreas

2011 ◽  
Vol 12 (1) ◽  
pp. 62 ◽  
Author(s):  
Jonathon T Hill ◽  
Keith R Anderson ◽  
Teresa L Mastracci ◽  
Klaus H Kaestner ◽  
Lori Sussel
Keyword(s):  
Protein Binding ◽  
Computational Analysis ◽  
Array Data

scholarly journals Towards Inhibition of Vif-APOBEC3G Interaction: Which Protein to Target?

2010 ◽  
Vol 2010 ◽  
pp. 1-10 ◽  
Author(s):  
Iris Cadima-Couto ◽  
Joao Goncalves
Keyword(s):  
Antiviral Activity ◽  
Protein Binding ◽  
Mechanism Of Action ◽  
Cellular Immunity ◽  
Viral Infectivity ◽  
Binding Partners ◽  
Viral Infectivity Factor ◽  
Vif Protein ◽  
Hiv 1 ◽  
Antiretroviral Activity

APOBEC proteins appeared in the cellular battle against HIV-1 as part of intrinsic cellular immunity. The antiretroviral activity of some of these proteins is overtaken by the action of HIV-1 Viral Infectivity Factor (Vif) protein. Since the discovery of APOBEC3G (A3G) as an antiviral factor, many advances have been made to understand its mechanism of action in the cell and how Vif acts in order to counteract its activity. The mainstream concept is that Vif overcomes the innate antiviral activity of A3G by direct protein binding and promoting its degradation via the cellular ubiquitin/proteasomal pathway. Vif may also inhibit A3G through mechanisms independent of proteasomal degradation. Binding of Vif to A3G is essential for its degradation since disruption of this interaction is predicted to stimulate intracellular antiviral immunity. In this paper we will discuss the different binding partners between both proteins as one of the major challenges for the development of new antiviral drugs.

scholarly journals Environmental Restrictions: A New Concept Governing HIV-1 Spread Emerging from Integrated Experimental-Computational Analysis of Tissue-Like 3D Cultures

Cells ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1112 ◽  
Author(s):  
Samy Sid Ahmed ◽  
Nils Bundgaard ◽  
Frederik Graw ◽  
Oliver Fackler
Keyword(s):  
In Silico ◽  
Computational Analysis ◽  
Virus Transmission ◽  
Target Cells ◽  
Virus Spread ◽  
Transmission Modes ◽  
3D Collagen ◽  
Cell Densities ◽  
Hiv 1

HIV-1 can use cell-free and cell-associated transmission modes to infect new target cells, but how the virus spreads in the infected host remains to be determined. We recently established 3D collagen cultures to study HIV-1 spread in tissue-like environments and applied iterative cycles of experimentation and computation to develop a first in silico model to describe the dynamics of HIV-1 spread in complex tissue. These analyses (i) revealed that 3D collagen environments restrict cell-free HIV-1 infection but promote cell-associated virus transmission and (ii) defined that cell densities in tissue dictate the efficacy of these transmission modes for virus spread. In this review, we discuss, in the context of the current literature, the implications of this study for our understanding of HIV-1 spread in vivo, which aspects of in vivo physiology this integrated experimental–computational analysis takes into account, and how it can be further improved experimentally and in silico.

scholarly journals RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases

2009 ◽  
Vol 37 (Database) ◽  
pp. D369-D373 ◽  
Author(s):  
A. Shulman-Peleg ◽  
R. Nussinov ◽  
H. J. Wolfson
Keyword(s):  
Protein Binding ◽  
Binding Pockets ◽  
Nucleotide Bases

Stem of SL1 RNA in HIV-1:  Structure and Nucleocapsid Protein Binding for a 1 × 3 Internal Loop†,‡

Biochemistry ◽  
2003 ◽  
Vol 42 (18) ◽  
pp. 5259-5269 ◽  
Author(s):  
YiQiong Yuan ◽  
Deborah J. Kerwood ◽  
Andrew C. Paoletti ◽  
Michael F. Shubsda ◽  
Philip N. Borer
Keyword(s):  
Protein Binding ◽  
Nucleocapsid Protein ◽  
Internal Loop ◽  
Hiv 1

Incorporation of side chain flexibility into protein binding pockets using MTflex

2016 ◽  
Vol 24 (20) ◽  
pp. 4978-4987 ◽  
Author(s):  
Nupur Bansal ◽  
Zheng Zheng ◽  
Kenneth M. Merz
Keyword(s):  
Protein Binding ◽  
Side Chain ◽  
Chain Flexibility ◽  
Binding Pockets

scholarly journals Sensitive Detection of Protein Binding to the Plasma Membrane with Dual-Color Z-Scan Fluorescence

2019 ◽  
Author(s):  
I. Angert ◽  
S.R. Karuka ◽  
J. Hennen ◽  
Y. Chen ◽  
J.P. Albanesi ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Protein Binding ◽  
Fibroblast Growth Factor Receptor ◽  
Detection Threshold ◽  
Growth Factor Receptor ◽  
Living Cells ◽  
Dual Color ◽  
Peripheral Membrane Protein ◽  
Order Of Magnitude ◽  
Hiv 1

ABSTRACTDelicate and transitory protein engagement at the plasma membrane (PM) is crucial to a broad range of cellular functions including cell motility, signal transduction, and virus replication. Here we describe a dual color (DC) extension of the fluorescence z-scan technique which has proven successful for quantification of peripheral membrane protein binding to the PM in living cells. We demonstrate that the co-expression of a second distinctly colored fluorescent protein provides a soluble reference species, which delineates the extent of the cell cytoplasm and lowers the detection threshold of z-scan PM binding measurements by an order of magnitude. DC z-scan generates an intensity profile for each detection channel that contains information on the axial distribution of the peripheral membrane and reference protein. Fit models for DC z-scan are developed and verified using simple model systems. Next, we apply the quantitative DC z-scan technique to investigate the binding of two peripheral membrane protein systems for which previous z-scan studies failed to detect binding: human immunodeficiency virus type 1 (HIV-1) matrix (MA) protein and lipidation-deficient mutants of the fibroblast growth factor receptor substrate 2α. Our findings show that these mutations severely disrupt PM association of fibroblast growth factor receptor substrate 2α but do not eliminate it. We further detected binding of HIV-1 MA to the PM using DC z-scan. Interestingly, our data indicate that HIV-1 MA binds cooperatively to the PM with a dissociation coefficient of Kd ~16 μM and Hill coefficient of n ~2.SIGNIFICANCEProtein binding to the plasma membrane of cells plays an important role in a multitude of cell functions and disease processes. Quantitative binding studies of protein/membrane interactions are almost exclusively limited to in vitro systems and may produce results that poorly mimic the authentic interactions in living cells. We report quantitative measurements of plasma membrane binding directly in living cells by using dual color z-scan fluorescence, which improves the detection threshold by an order of magnitude compared to our previous single color technique. This advance allowed us to examine the role of mutations on binding affinity and identify the presence of cooperative binding in protein systems with relevance to HIV/AIDS and cancer biology.

scholarly journals Free enthalpies of replacing water molecules in protein binding pockets

2012 ◽  
Vol 26 (12) ◽  
pp. 1293-1309 ◽  
Author(s):  
Sereina Riniker ◽  
Luzi J. Barandun ◽  
François Diederich ◽  
Oliver Krämer ◽  
Andreas Steffen ◽  
...  
Keyword(s):  
Protein Binding ◽  
Water Molecules ◽  
Binding Pockets
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