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Taking the opportunity of the 20th anniversary of the word "proteomics", this young adult age is a good time to remember how proteomics came from enormous progress in protein separation and protein microanalysis techniques, and from the…
Cell wall proteins are essential constituents of plant cell walls; they are involved in modifications of cell wall components, wall structure, signaling and interactions with plasma membrane proteins at the cell surface. The application of…
Linguistic analysis of protein sequences is an underexploited technique. Here, we capitalize on the concept of the lipogram to characterize sequences at the proteome levels. A lipogram is a literary composition which omits one or more…
Identification and characterization of large protein complexes is a mainstay of biochemical toolboxes. Utilization of cross-linking chemicals can facilitate the capture and identification of transient or weak interactions of a transient…
We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of the cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic…
Phase separation is as familiar as watching vinegar separating from oil in vinegrette. The observation that phase separation of proteins and nucleic acids is widespread in living cells has opened an entire field of research into the…
We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for…
Efficient bacterial chromosome segregation typically requires the coordinated action of a three-components, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the…
Proteins perform nearly all cellular functions and constitute most drug targets, making their analysis fundamental to understanding human biology in health and disease. Tandem mass spectrometry (MS$^2$) is the major analytical technique in…
Electrochemistry exploits local current heterogeneities at various scales ranging from the micrometer to the nanometer. The last decade has witnessed unprecedented progress in the development of a wide range of electroanalytical techniques…
Molecular dynamics using atomistic modeling is frequently used to unravel the mechanisms of macroion release from electrosprayed droplets. However, atomistic modeling is currently feasible for only the smallest window of droplet sizes…
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance…
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Multiple technologies that measure expression levels of protein mixtures in the human body offer a potential for detection and understanding the disease. The recent increase of these technologies prompts researchers to evaluate the…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
Rationale: In a shotgun proteomics experiment with data-dependent acquisition, real-time analysis of a precursor scan results in selection of a handful of peaks for subsequent isolation, fragmentation and secondary scanning. This peak…
Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereo-isomers, even at very low temperatures. In this paper we discuss the different approaches for the manipulation of the motion of…
We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…
Multi-step assembly of individual protein building blocks is key to the formation of essential higher-order structures inside and outside of cells. Optical tweezers is a technique well suited to investigate the mechanics and dynamics of…