A million peptide motifs for the molecular biologist

P Tompa, NE Davey, TJ Gibson, MM Babu - Molecular cell, 2014 - cell.com
A molecular description of functional modules in the cell is the focus of many high-
throughput studies in the postgenomic era. A large portion of biomolecular interactions in …

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

G Wei, W **, 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 …

Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation

K Van Roey, B Uyar, RJ Weatheritt, H Dinkel… - Chemical …, 2014 - ACS Publications
The eukaryotic cell is a bustling collection of macromolecules acting cooperatively to
mediate the functions required for cell viability. Specific, context-dependent and tightly …

Evolution of two-component signal transduction systems

EJ Capra, MT Laub - Annual review of microbiology, 2012 - annualreviews.org
To exist in a wide range of environmental niches, bacteria must sense and respond to a
variety of external signals. A primary means by which this occurs is through two-component …

[LIVRE][B] An introduction to systems biology: design principles of biological circuits

U Alon - 2019 - api.taylorfrancis.com
Praise for the first edition:… superb, beautifully written and organized work that takes an
engineering approach to systems biology. Alon provides nicely written appendices to …

Foundations for engineering biology

D Endy - Nature, 2005 - nature.com
Engineered biological systems have been used to manipulate information, construct
materials, process chemicals, produce energy, provide food, and help maintain or enhance …

Programmable design of orthogonal protein heterodimers

Z Chen, SE Boyken, M Jia, F Busch, D Flores-Solis… - Nature, 2019 - nature.com
Specificity of interactions between two DNA strands, or between protein and DNA, is often
achieved by varying bases or side chains coming off the DNA or protein backbone—for …

Contextualizing context for synthetic biology–identifying causes of failure of synthetic biological systems

S Cardinale, AP Arkin - Biotechnology journal, 2012 - Wiley Online Library
Despite the efforts that bioengineers have exerted in designing and constructing biological
processes that function according to a predetermined set of rules, their operation remains …

Interactions by disorder–a matter of context

K Bugge, I Brakti, CB Fernandes, JE Dreier… - Frontiers in Molecular …, 2020 - frontiersin.org
Living organisms depend on timely and organized interactions between proteins linked in
interactomes of high complexity. The recent increased precision by which protein …

Response to hyperosmotic stress

H Saito, F Posas - Genetics, 2012 - academic.oup.com
An appropriate response and adaptation to hyperosmolarity, ie., an external osmolarity that
is higher than the physiological range, can be a matter of life or death for all cells. It is …