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• W2085697834 abstract "Understanding the process of protein folding has been recognized as an important challenge for >70 years. It is, quintessentially, a thermodynamic problem and, arguably, thermodynamics is our most powerful discipline for understanding biological systems. Yet, despite all this, we still lack predictive understanding of protein folding. Is something missing from this picture? Understanding the process of protein folding has been recognized as an important challenge for >70 years. It is, quintessentially, a thermodynamic problem and, arguably, thermodynamics is our most powerful discipline for understanding biological systems. Yet, despite all this, we still lack predictive understanding of protein folding. Is something missing from this picture? The idea that the polypeptide chain can fold into multiple, mutually exclusive, meta-stable conformations, raising the question of why a folded protein has only one native conformation. A proposed solution to the question raised by chain frustration, namely, the energy of all alternative conformations is separated from that of the native fold by a large, highly unfavorable gap in energy. A graphic depiction of a population of folding proteins. The favorable-high-entropy, unfavorable-high-energy unfolded state is conceptualized as a wide funnel mouth, whereas the unfavorable-low-entropy, favorable-low-energy native state corresponds to a narrow funnel spout. Named after Professor N. Gō, who introduced it to reconcile the ostensibly competing contributions of short-range versus long-range interactions in proteins. The consistency principle proposes that energetic interactions at multiple length scales are consistent with the native conformation. Our restatement of the Gō consistency principle. There are two predominant energetically favorable regions for an alanyl dipeptide (see Figure 1 in main text); repeating backbone dihedral angles from these two regions result in segments of the two favorable hydrogen-bonded secondary structures, α helix and strands of β sheet. These secondary-structure segments interact favorably with one another, giving rise to super-secondary structure. Thus, short-range favorable interactions promote longer-range favorable interactions at successive levels of the structural hierarchy of a protein. A proposal as to why protein molecules, in which folding is guided by numerous energetic interactions at multiple length scales, adopt one predominant native conformation. (See Gō consistency principle.) The fundamental connection between arithmetic and geometry. There is a one-to-one correspondence between the set of all real numbers and a 1D line; that is, any real number corresponds to a unique point on the line and, conversely, any point on the line corresponds to a unique real number. Similar to Brownian motion, but with the further restriction that the path cannot cross itself. Specifically for proteins, a polypeptide chain path in 3D space in which there is no directional correlation between any two, arbitrarily chosen chain segments, and with the further restriction that the chain cannot pass through itself. Akin to absolute rate theory for small-molecule chemical reactions. The transition-state species is pictured at the top of an energy barrier separating U(nfolded) from N(ative). The experimental goal is to identify those residues that comprise the organizational ‘tipping point’ (the transition state)." @default.
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• W2085697834 date "2005-02-01" @default.
• W2085697834 modified "2023-09-25" @default.
• W2085697834 title "Are proteins made from a limited parts list?" @default.
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• W2085697834 doi "https://doi.org/10.1016/j.tibs.2004.12.005" @default.
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