Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism

I attempt to reconcile apparently conflicting factors and mechanisms that have been proposed to determine the rate constant for two-state folding of small proteins, on the basis of general features of the structures of transition states. Φ-Value analysis implies a transition state for folding that resembles an expanded and distorted native structure, which is built around an extended nucleus. The nucleus is composed predominantly of elements of partly or well-formed native secondary structure that are stabilized by local and long-range tertiary interactions. These long-range interactions give rise to connecting loops, frequently containing the native loops that are poorly structured. I derive an equation that relates differences in the contact order of a protein to changes in the length of linking loops, which, in turn, is directly related to the unfavorable free energy of the loops in the transition state. Kinetic data on loop extension mutants of CI2 and α-spectrin SH3 domain fit the equation qualitatively. The rate of folding depends primarily on the interactions that directly stabilize the nucleus, especially those in native-like secondary structure and those resulting from the entropy loss from the connecting loops, which vary with contact order. This partitioning of energy accounts for the success of some algorithms that predict folding rates, because they use these principles either explicitly or implicitly. The extended nucleus model thus unifies the observations of rate depending on both stability and topology.

International Coffee Agreement 1968, as extended : report to accompany Ex. O, 93-1 /

At head of title: 93d Congress, 1st session, Senate, Executive report ; no. 93-16.

International Conference on the Physics of X-Ray Spectra program and extended abstracts.

Mode of access: Internet.

Medical Advisory Committee report and recommendations on the administration of the OASI disability freeze provision : preservation of rights of individuals with extended total disability, Social security amendments of l954.

"July 1955."

An Evaluation of the feasibility of a substate area extended benefit program : final report.

"This report was prepared for the Unemployment Insurance Service, U.S. Department of Labor under Contract Number 99-7-0805-04-138-01 with Mathematica Policy Research, Inc. The authors of this report are John L. Czajka, Sharon K. Long and Walter Nicholson ..."

Geometry of profiles across Inner Continental Shelves of the Atlantic and Gulf coasts of the United States /

Along most of the U.S. east and gulf coasts from Long Island to the Mexican Border, bottom profiles extending over the Inner Continental Shelves normal from the coast display a characteristic two-sector shape. Near the coast, the 'shoreface' profile sector is steep and concave-up; the seaward 'ramp' sector is planar with a gradual slope away from the coast. As part of the Beach Evaluation Program at this Center, 9 profiles extending from the coast 30.5 km (19 miles) seaward at each of 49 localities were averaged to mathematically characterize the profiles and to develop and test criteria for discriminating among groups of profiles. Results indicate Inner Continental Shelf profiles can be mathematically defined by 4 parameters: a = ramp slope (0 - 0.00107); b = depth of the ramp at the shoreline, when the ramp is extended as a straight line below the shoreface sector (0 - 24.7 meters, 0 - 81 feet); c = distance from the shoreline to the shoreface-ramp boundary (0.2 - 20.6 km, 0.12 - 12.9 miles); and f = index of concavity of the shoreface sector (0.21 - 1.72). Values in parentheses are the range of values obtained for the 49 averaged profiles. An equation was developed to define bottom depth as a function of distance from shore incorporating these four parameters. Computed depths using the equation were found to be generally within 5% of actual profile depths. In most cases, no relationship was found between the geometric characteristics of the shoreface and the ramp.

Department of Medicine and Surgery census data for extended care facilities, 1967-1975 /

Bibliography: p. 20.

Report of the Joint legislative committee to investigate the administration and enforcement of the law. Pursuant to resolution of May 7, 1937, extended to March 1, 1939 [and Exhibits referred to but not included in report and public hearings]

John J. McNaboe, chairman. His autograph presentation copy to Col. Desmond O'Keefe.

Beyond poverty : extended measures of well-being, 1992 /

Mode of access: Internet.

A versatile high-voltage bias supply for extended range MIS C(V) and G(V) measurements /

Includes bibliographical references (p. 61).

Delays in recomputing social security benefits cause underpayments for extended periods : report /

"B215803"--Prelim. p.

An analysis of the 1981-82 changes in the extended benefit program.

"Prepared by Walter Corson ... and Walter Nicholson ... The research was sponsored by the Office of Strategic Planning and Policy Development of the Employment and Training Administration."

Improper use of industrial funds by Defense extended the life of appropriations which otherwise would have expired : report to the chairman, Committee on Appropriations, House of Representatives /

"B-214645"--P. [1] (1st group)

Federal employees : OPM data do not identify if temporary employees work for extended periods : report to Congressional Requesters /

"GAO-02-296."

The Punjab civil law manual : notes on the Punjab Laws Act and the enactments extended to Punjab by that act, and also on the customary Hindu and Muhammedan law as applicable to the Punjab /

Mode of access: Internet.