A Buried Ionizable Residue Destabilizes the Native State and the Transition State in the Folding of Monellin

Biochemistry ◽  
2012 ◽  
Vol 51 (45) ◽  
pp. 9058-9066 ◽  
Author(s):  
Nilesh Aghera ◽  
Ishita Dasgupta ◽  
Jayant B. Udgaonkar
Keyword(s):  
Transition State ◽  
Native State ◽  
Ionizable Residue

The unfolding transition state of ubiquitin with charged residues has higher energy than that with hydrophobic residues

2020 ◽  
Vol 22 (40) ◽  
pp. 23158-23168
Author(s):  
Tathagata Nandi ◽  
Amogh Desai ◽  
Sri Rama Koti Ainavarapu
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Transition State ◽  
State Structure ◽  
Native State ◽  
Hydrophobic Residues ◽  
Folding Pathways ◽  
Charged Residues

The native-state structure and folding pathways of a protein are encoded in its amino acid sequence.

scholarly journals Force Dependence of Proteins’ Transition State Position and the Bell–Evans Model

Nanomaterials ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3023
Author(s):  
Marc Rico-Pasto ◽  
Annamaria Zaltron ◽  
Felix Ritort
Keyword(s):  
Transition State ◽  
Single Molecule ◽  
High Energy ◽  
High Temporal Resolution ◽  
Native State ◽  
Force Extension ◽  
Single Molecule Force Spectroscopy ◽  
Large Hysteresis ◽  
Kinetic Rates ◽  
State Position

Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and measure their free energy landscape. The force–extension curves of single proteins often present large hysteresis, with unfolding forces that are higher than refolding ones. Therefore, the high energy of the transition state (TS) in these molecules precludes kinetic rates measurements in equilibrium hopping experiments. In irreversible pulling experiments, force-dependent kinetic rates measurements show a systematic discrepancy between the sum of the folding and unfolding TS distances derived by the kinetic Bell–Evans model and the full molecular extension predicted by elastic models. Here, we show that this discrepancy originates from the force-induced movement of TS. Specifically, we investigate the highly kinetically stable protein barnase, using pulling experiments and the Bell–Evans model to characterize the position of its kinetic barrier. Experimental results show that while the TS stays at a roughly constant distance relative to the native state, it shifts with force relative to the unfolded state. Interestingly, a conversion of the protein extension into amino acid units shows that the TS position follows the Leffler–Hammond postulate: the higher the force, the lower the number of unzipped amino acids relative to the native state. The results are compared with the quasi-reversible unfolding–folding of a short DNA hairpin.

A Dry Transition State More Compact Than the Native State Is Stabilized by Non-Native Interactions during the Unfolding of a Small Protein

Biochemistry ◽  
2017 ◽  
Vol 56 (29) ◽  
pp. 3699-3703 ◽  
Author(s):  
Sreemantee Sen ◽  
Rama Reddy Goluguri ◽  
Jayant B. Udgaonkar
Keyword(s):  
Transition State ◽  
Native State ◽  
Small Protein

Existence of DNA in yeast microbodies

1978 ◽  
Vol 36 (2) ◽  
pp. 232-233
Author(s):  
Masako Osumi ◽  
Misuzu Nagano ◽  
Hiroko Kazama
Keyword(s):  
Catalase Activity ◽  
Buoyant Density ◽  
Model System ◽  
Contour Length ◽  
Native State ◽  
Normal Alkane ◽  
Remarkable Increase ◽  
Dna Molecule ◽  
Mitochondrial Dnas

We have found that microbodies appeared profusely together with a remarkable increase in catalase activity in normal alkane-grown cells of hydrocarbon-utilizing Candida yeasts, and that the microbodies multiplied by division in these cells. These features of Candida yeasts seem to provide a useful model system for studies on the biogenesis of the microbody. Subsequently, we have succeeded in isolation of Candida microbodies in an apparently native state, as judged biochemically and morphologically. The presence of DNA in the purified microbody fraction thus obtained was proved by the diphenylamine method. DNA molecule of about 15 urn in contour length was released from an isolated microbody. The physicochemical analyses of the microbody DNA revealed that its buoyant density differed from nuclear and mitochondrial DNAs. All these results lead us to the possibility that there is a novel type of DNA in microbodies.

Electron Microscopic Observation of Biological Specimens in Their Native State by Employing Cryogenic Techniques

1972 ◽  
Vol 30 ◽  
pp. 410-411 ◽  
Author(s):  
Tokio Nei ◽  
Haruo Yotsumoto ◽  
Yoichi Hasegawa ◽  
Yuji Nagasawa
Keyword(s):  
Electron Microscopic Observation ◽  
Surface Structures ◽  
Specimen Preparation ◽  
Native State ◽  
Electron Microscopic ◽  
Biological Specimen ◽  
Specimen Holder ◽  
Cold Stage ◽  
Preparation Techniques ◽  
Scanning Electron

In order to observe biological specimens in their native state, that is, still containing their water content, various methods of specimen preparation have been used, the principal two of which are the chamber method and the freeze method.Using its recently developed cold stage for installation in the pre-evacuation chamber of a scanning electron microscope, we have succeeded in directly observing a biological specimen in its frozen state without the need for such conventional specimen preparation techniques as drying and metallic vacuum evaporation. (Echlin, too, has reported on the observation of surface structures using the same freeze method.)In the experiment referred to herein, a small sliced specimen was place in the specimen holder. After it was rapidly frozen by freon cooled with liquid nitrogen, it was inserted into the cold stage of the specimen chamber.

Memapsin 2, a drug target for Alzheimer's disease

2003 ◽  
Vol 70 ◽  
pp. 213-220 ◽  
Author(s):  
Gerald Koelsch ◽  
Robert T. Turner ◽  
Lin Hong ◽  
Arun K. Ghosh ◽  
Jordan Tang
Keyword(s):  
Crystal Structure ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Transition State ◽  
Amyloid Precursor Protein ◽  
Therapeutic Target ◽  
Drug Target ◽  
Aspartic Protease ◽  
Precursor Protein ◽  
Memapsin 2

Mempasin 2, a ϐ-secretase, is the membrane-anchored aspartic protease that initiates the cleavage of amyloid precursor protein leading to the production of ϐ-amyloid and the onset of Alzheimer's disease. Thus memapsin 2 is a major therapeutic target for the development of inhibitor drugs for the disease. Many biochemical tools, such as the specificity and crystal structure, have been established and have led to the design of potent and relatively small transition-state inhibitors. Although developing a clinically viable mempasin 2 inhibitor remains challenging, progress to date renders hope that memapsin 2 inhibitors may ultimately be useful for therapeutic reduction of ϐ-amyloid.

Collisional dynamics of Ca1D + HBr reactions: evidence for transition-state motions

1999 ◽  
Vol 97 (8) ◽  
pp. 967-976 ◽  
Author(s):  
M. Garay Salazar, J. M. Orea Rocha, A.
Keyword(s):  
Transition State ◽  
Collisional Dynamics
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