Topic
Sequence hypothesis
About: Sequence hypothesis is a research topic. Over the lifetime, 70 publications have been published within this topic receiving 1998 citations.
Papers published on a yearly basis
Papers
TL;DR: The N-terminal 72 residues of an integral membrane fragment, P5, of the human erythrocyte anion-transport protein, was shown to have the following amino acid sequence that forms two transmembrane alpha-helices, which could comprise that part of the protein responsible for transport activity.
Abstract: The N-terminal 72 residues of an integral membrane fragment, P5, of the human erythrocyte anion-transport protein, which is known to be directly involved in the anion-exchange process, was shown to have the following amino acid sequence: Met-Val-Pro-Lys-Pro-Gln-Gly-Pro-Leu-Pro-Asn-Thr-Ala-Leu-Leu-Ser-Leu-Val-Leu-Met -Ala-Gly-Thr-Phe-Phe-Phe-Ala-Met-Met-Leu-Arg-Lys-Phe-Lys-Asn-Ser-Ser-Tyr-Phe-Pro-Gly-Lys-Leu-Arg-Arg-Val-Ile-Gly-Asp-Phe-Gly-Val-Pro-Ile-Ser-Ile-Leu-Ile-Met-Val-Leu-Val-Asp-Phe-Phe-Ile-Gln-Asp-Thr-Tyr-Thr-Gln- The structure of this fragment was analysed, with account being taken of the constraints that apply to the folding of integral membrane proteins and the topographical locations of various sites in the sequence. It was concluded that this sequence forms two transmembrane alpha-helices. These are probably part of a cluster of amphipathic transmembrane alpha-helices, which could comprise that part of the protein responsible for transport activity. The presently available evidence relating to the anion-exchange process was considered with the structural features noted in this study and a possible molecular mechanism is proposed. In this model the rearrangement of a network of intramembranous charged pairs mediates the translocation of an anion between anion-binding regions at each surface of the membrane, which are composed of clusters of positively charged amino acids. This model imposes a sequential exchange mechanism on the system. Supplementary material, including Tables and Figures describing the compositions of peptides determined by amino acid analysis and sequence studies, quantitative and qualitative data that provide a residue-by-residue justification for the sequence assignment and a description of modifications to and use of the solid-phase sequencer has been deposited as Supplementary Publication SUP 50123 (12 pages) with the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained as indicated in Biochem. J. (1983) 209, 5.
102 citations
TL;DR: The chapter concludes that there have been dramatic developments in this field and it now seems possible that the code of the genetic code will be found within a comparatively short time.
Abstract: Publisher Summary The Sequence Hypothesis states that the amino acid sequence of a protein is determined by the sequence of nucleotides in some particular piece of nucleic acid. The evidence in favor of this is now very considerable, and hopes that this relationship may be a simple one and that the sequence of the four bases in the nucleic acid can be thought of as a simple code for the amino acid sequence. The exact sequence of bases that determines each of the twenty amino acids found in proteins is known as the “coding problem.” The amount of degeneracy may be small andthe evidence from the cell-free system, the amino acid replacement data, and the fractionation of sRNA, is compatible with this. The amount of degeneracy may be very much higher and this is suggested by the wide range of DNA composition and by the genetic studies. Also,it is not contradicted by the more direct evidence, though this suggests that if the code is highly degenerate it is unlikely to be degenerate at random. The chapter concludes that there have been dramatic developments in this field and it now seems possible that the code will be found within a comparatively short time. The chapter deals with the recent progress and discusses the general nature of the genetic code.
84 citations
TL;DR: It is concluded that rather than life having explored only an infinitesimally small part of sequence space in the last 4 Gyr, it is instead quite plausible for all of functional protein sequence space to have been explored and that furthermore, at the molecular level, there is no role for contingency.
Abstract: We suggest that the vastness of protein sequence space is actually completely explorable during the populating of the Earth by life by considering upper and lower limits for the number of organisms, genome size, mutation rate and the number of functionally distinct classes of amino acids. We conclude that rather than life having explored only an infinitesimally small part of sequence space in the last 4 Gyr, it is instead quite plausible for all of functional protein sequence space to have been explored and that furthermore, at the molecular level, there is no role for contingency.
81 citations
Patent•
28 Apr 2010
TL;DR: In this article, the authors present an approach for calling variations in a sample polynucleotide sequence compared to a reference polynotide sequence. But the approach is limited to the case where a likelihood exists that one or more bases of the sample polyclotide sequence are changed from corresponding bases in the reference polyclonal sequence.
Abstract: Embodiments for calling variations in a sample polynucleotide sequence compared to a reference polynucleotide sequence are provided. Aspects of the embodiments include executing an application on at least one computer that locates local areas in the reference polynucleotide sequence where a likelihood exists that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence, where the likelihood is determined at least in part based on mapped mated reads of the sample polynucleotide sequence; generating at least one sequence hypothesis for each of the local areas, and optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses of high probability for the local areas; and analyzing the optimized sequence hypotheses to identify a series of variation calls in the sample polynucleotide sequence.
61 citations
TL;DR: A knowledge‐based approach for determining the effective interactions between amino acids based on amino acid type, their secondary structure, and the contact based environment that they find themselves in the native state structure as measured by their number of neighbors is presented.
Abstract: Understanding the key factors that influence the interaction preferences of amino acids in the folding of proteins have remained a challenge. Here we present a knowledge-based approach for determining the effective interactions between amino acids based on amino acid type, their secondary structure, and the contact based environment that they find themselves in the native state structure as measured by their number of neighbors. We find that the optimal information is approximately encoded in a 60 x 60 matrix describing the 20 types of amino acids in three distinct secondary structures (helix, beta strand, and loop). We carry out a clustering scheme to understand the similarity between these interactions and to elucidate a nonredundant set. We demonstrate that the inferred energy parameters can be used for assessing the fit of a given sequence into a putative native state structure.
61 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2019 | 1 |
| 2017 | 1 |
| 2016 | 2 |
| 2015 | 3 |
| 2014 | 2 |
| 2013 | 2 |