Nonspecific binding—fundamental concepts and consequences for biosensing applications

A Frutiger, A Tanno, S Hwu, RF Tiefenauer… - Chemical …, 2021 - ACS Publications
Nature achieves differentiation of specific and nonspecific binding in molecular interactions
through precise control of biomolecules in space and time. Artificial systems such as …

Intrinsically disordered proteins and their “mysterious”(meta) physics

VN Uversky - Frontiers in Physics, 2019 - frontiersin.org
Recognition of the natural abundance and functional importance of intrinsically disordered
proteins (IDPs), and protein hybrids that contain both intrinsically disordered protein regions …

Insights into protein–ligand interactions: mechanisms, models, and methods

X Du, Y Li, YL Xia, SM Ai, J Liang, P Sang… - International journal of …, 2016 - mdpi.com
Molecular recognition, which is the process of biological macromolecules interacting with
each other or various small molecules with a high specificity and affinity to form a specific …

Impact of protein conformational diversity on AlphaFold predictions

T Saldaño, N Escobedo, J Marchetti, DJ Zea… - …, 2022 - academic.oup.com
Motivation After the outstanding breakthrough of AlphaFold in predicting protein 3D models,
new questions appeared and remain unanswered. The ensemble nature of proteins, for …

The role of protein loops and linkers in conformational dynamics and allostery

E Papaleo, G Saladino, M Lambrughi… - Chemical …, 2016 - ACS Publications
Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review

P Csermely, T Korcsmáros, HJM Kiss, G London… - Pharmacology & …, 2013 - Elsevier
Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …

Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W Xi, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

[HTML][HTML] Allostery in disease and in drug discovery

R Nussinov, CJ Tsai - Cell, 2013 - cell.com
Allostery is largely associated with conformational and functional transitions in individual
proteins. This concept can be extended to consider the impact of conformational …

[HTML][HTML] Passive immunotherapies targeting Aβ and tau in Alzheimer's disease

SS Plotkin, NR Cashman - Neurobiology of Disease, 2020 - Elsevier
Amyloid-β (Aβ) and tau proteins currently represent the two most promising targets to treat
Alzheimer's disease. The most extensively developed method to treat the pathologic forms of …

Ras conformational ensembles, allostery, and signaling

S Lu, H Jang, S Muratcioglu, A Gursoy, O Keskin… - Chemical …, 2016 - ACS Publications
Ras proteins are classical members of small GTPases that function as molecular switches by
alternating between inactive GDP-bound and active GTP-bound states. Ras activation is …