Insight into RIPK4 mutations I121N and T184I involved in popliteal pterygium syndrome lethal type using computational methods

Background: Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Objective: Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. Conclusion: There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.

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Popliteal pterygium syndrome with unusual features

The Indian Journal of Pediatrics ◽

10.1007/bf02724282 ◽

2004 ◽

Vol 71 (3) ◽

pp. 269-270 ◽

Cited By ~ 1

Author(s):

C. K. Sasidharan ◽

K. V. Ravi

Keyword(s):

Popliteal Pterygium Syndrome ◽

Popliteal Pterygium

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Endoscopic Release of Intraoral Synechiae in Popliteal Pterygium Syndrome

Annals of Plastic Surgery ◽

10.1097/00000637-200211000-00018 ◽

2002 ◽

Vol 49 (5) ◽

pp. 550-552 ◽

Cited By ~ 2

Author(s):

Fabrizio Schonauer ◽

Ivan La Rusca ◽

Desiree Sordino ◽

Alessandro Settimi ◽

Guido Molea

Keyword(s):

Endoscopic Release ◽

Popliteal Pterygium Syndrome ◽

Popliteal Pterygium

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Popliteal pterygium syndrome

Oral Surgery Oral Medicine Oral Pathology ◽

10.1016/0030-4220(87)90333-1 ◽

1987 ◽

Vol 63 (1) ◽

pp. 17-20 ◽

Cited By ~ 6

Author(s):

Barry Steinberg ◽

Vernon Saunders

Keyword(s):

Popliteal Pterygium Syndrome ◽

Popliteal Pterygium

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Popliteal pterygium syndrome in a Swedish family-clinical findings and genetic analysis with the van der Woude syndrome locus at 1q32-q41

Acta Odontologica Scandinavica ◽

10.1080/000163500429334 ◽

2000 ◽

Vol 58 (2) ◽

pp. 85-88 ◽

Cited By ~ 7

Author(s):

Fung Ki Wong ◽

Britt Gustafsson

Keyword(s):

Genetic Analysis ◽

Clinical Findings ◽

Van Der Woude Syndrome ◽

Swedish Family ◽

Popliteal Pterygium Syndrome ◽

Popliteal Pterygium

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Popliteal Pterygium Syndrome with Special Consideration of the Cleft Malformation: Case Report

The Cleft Palate-Craniofacial Journal ◽

10.1597/1545-1569_1992_029_0080_ppswsc_2.3.co_2 ◽

1992 ◽

Vol 29 (1) ◽

pp. 80-84 ◽

Cited By ~ 1

Author(s):

Hubertus Koch ◽

Magdalena Grzonka ◽

Josef Koch

Keyword(s):

Case Report ◽

Treatment Protocol ◽

Special Consideration ◽

Upper Lip ◽

Popliteal Pterygium Syndrome ◽

Popliteal Pterygium

This report describes a new case of popliteal pterygium syndrome (PPS) and also a treatment protocol. The patient presented with the complete complex of PPS and additional abnormalities that have not been described in the literature: a sinus of the upper lip, an extreme hypopoplastic prolabium with aplasia of the vestibule In this area, and a velar pterygium.

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Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

International Journal of Molecular Sciences ◽

10.3390/ijms19113401 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3401 ◽

Cited By ~ 16

Author(s):

Ashutosh Srivastava ◽

Tetsuro Nagai ◽

Arpita Srivastava ◽

Osamu Miyashita ◽

Florence Tama

Keyword(s):

Protein Dynamics ◽

Computational Methods ◽

Protein Structures ◽

Three Dimensional ◽

Dimensional Structure ◽

X Ray ◽

X Ray Crystallography ◽

Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

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