Uncovering protein structure

Stollar, Elliott J.; Smith, David P.

doi:10.1042/ebc20190042

Cited by 60 publications

(56 citation statements)

References 9 publications

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“…These include egg, milk, animal meat, and fish flesh proteins, as well as proteins from some plant sources such as those from soy and derived products. [2] Due to their different size and tridimensional structure, [3] proteins hugely vary in their properties such as water solubility, amphiphilicity, digestibility in the human digestive tract, net charge (depending on surrounding pH and the protein's isoelectric point (pI)), and interaction of parts of their structure (e.g., hydrophobic pockets) with other molecules. [4,5] Proteins may also contain nonamino acid components, including, for example, phosphorous and calcium, and plant proteins can be tightly associated with secondary plant compounds such as flavonoids/isoflavonoids, lectins, saponins, and phytates.…”

Section: Introductionmentioning

confidence: 99%

Influence of Proteins on the Absorption of Lipophilic Vitamins, Carotenoids and Curcumin – A Review

Iddir

Vahid

Merten

et al. 2022

Molecular Nutrition Food Res

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While proteins have been widely used to encapsulate, protect, and regulate the release of bioactive food compounds, little is known about the influence of co-consumed proteins on the absorption of lipophilic constituents following digestion, such as vitamins (A, D, E, K), carotenoids, and curcumin. Their bioavailability is often low and very variable, depending on the food matrix and host factors. Some proteins can act as emulsifiers during digestion. Their liberated peptides have amphiphilic properties that can facilitate the absorption of microconstituents, by improving their transition from lipid droplets into mixed micelles. Contrarily, the less well digested proteins could negatively impinge on enzymatic accessibility to the lipid droplets, slowing down their processing into mixed micelles and entrapping apolar food compounds. Interactions with mixed micelles and proteins are also plausible, as shown earlier for drugs. This review focuses on the ability of proteins to act as effective emulsifiers of lipophilic vitamins, carotenoids, and curcumin during digestion. The functional properties of proteins, their chemical interactions with enzymes and food constituents during gastro-intestinal digestion, potentials and limitations for their use as emulsifiers are emphasized and data from human, animal, and in vitro trials are summarized.

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Section: Introductionmentioning

confidence: 99%

Influence of Proteins on the Absorption of Lipophilic Vitamins, Carotenoids and Curcumin – A Review

Iddir

Vahid

Merten

et al. 2022

Molecular Nutrition Food Res

View full text Add to dashboard Cite

show abstract

“…The history of protein structure prediction problem goes back to the determination of the 3D structure of myoglobin by John Kendrew in the 1950s which was a landmark in biochemistry and structural biology 10 . Since then, X-ray crystallography has become the gold-standard experimental method for protein structure determination 11 , 12 , as well as the reference to validate computational models for protein structure prediction. Considering the high cost and technical limitations of X-ray crystallography, and the growing access to biological sequences following the Human Genome Project, predicting the 3D structure of a protein from its sequence became the Mount Everest in computational biology 8 ; a challenge broadly known as the “protein folding problem”.…”

Section: Paradigm Shifting Successes Of DLmentioning

confidence: 99%

Current progress and open challenges for applying deep learning across the biosciences

et al. 2022

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Deep Learning (DL) has recently enabled unprecedented advances in one of the grand challenges in computational biology: the half-century-old problem of protein structure prediction. In this paper we discuss recent advances, limitations, and future perspectives of DL on five broad areas: protein structure prediction, protein function prediction, genome engineering, systems biology and data integration, and phylogenetic inference. We discuss each application area and cover the main bottlenecks of DL approaches, such as training data, problem scope, and the ability to leverage existing DL architectures in new contexts. To conclude, we provide a summary of the subject-specific and general challenges for DL across the biosciences.

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“…Both the native and unfolded states are highly heterogeneous. Spontaneous self-assembly (folding) of most homochiral proteins into NS occurs at a very short time interval (in the order of 10 −6 to 10 −1 s) [ 82 , 83 ]. Rapid folding to NS prevents the impact of unwonted spontaneous racemization, which is, generally, a much slower process.…”

Section: Entropymentioning

confidence: 99%

Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality

Dyakin

Uversky

2022

IJMS

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Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.

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Uncovering protein structure

Cited by 60 publications

References 9 publications

Influence of Proteins on the Absorption of Lipophilic Vitamins, Carotenoids and Curcumin – A Review

Influence of Proteins on the Absorption of Lipophilic Vitamins, Carotenoids and Curcumin – A Review

Current progress and open challenges for applying deep learning across the biosciences

Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality

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