How Do Hydrogen Bonds Contribute to Protein-DNA Recognition?

Abstract The average strength of hydrogen bonding interactions at the interface of 40 protein-DNA complexes comprising ∼ 1500 potential hydrogen bonds and their free energies of formation have been estimated employing some recent advances in theoretical treatments of electrostatic interactions. The hydrogen bond spatial frequency distribution shows a maximum at a proton-acceptor distance of 2.1Å. The corresponding average interaction energy and the binding free energy are computed to be -1 kcal and +4 kcal/mol.H-bond respectively. Thus hydrogen bonds do not appear to provide the driving force for the formation of specific complexes from initially separated protein and DNA but serve to optimize the interactions in the specific complex once it is formed, via distance and angle requirements.

Infant feeding practices of mothers in an urban area in Nepal

BACKGROUND

Child health in developing countries including Nepal is a matter of serious concern as the prevalence of malnutrition among children continues to be high with 48.6% of children under five in Nepal being underweight. Since infant feeding practices adopted by mothers play a major role in influencing health of these children, there is a need to study the infant feeding practices prevalent in different areas in order to have pragmatic approaches to solve this problem.

MATERIALS AND METHODS

A cross sectional study was conducted among mothers who attended the immunization clinics of 18 wards of Pokhara municipality area. They were interviewed with a semi-structured questionnaire on various aspects of infant feeding.

RESULT

A total of 168 mothers were interviewed and prevalence of breastfeeding was 99.4% (167). Only 43.5% of the mothers initiated breastfeeding within one hour of birth and 60.5% were practicing exclusive breastfeeding at 5 months. Almost 40% of the mothers started complementary feeding before the recommended age of 6 months and 22.5 % delayed introduction of complementary feeding beyond the recommended age.

CONCLUSION

Breast feeding practices adopted by mothers of Pokhara urban area are still lacking in terms of late initiation of and early starting of complementary feeding. There is a need to educate the mothers regarding proper infant feeding practices.

Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level

Noncovalent association of proteins to specific target sites on DNA--a process central to gene expression and regulation--has thus far proven to be idiosyncratic and elusive to generalizations on the nature of the driving forces. The spate of structural information on protein--DNA complexes sets the stage for theoretical investigations on the molecular thermodynamics of binding aimed at identifying forces responsible for specific macromolecular recognition. Computation of absolute binding free energies for systems of this complexity transiting from structural information is a stupendous task. Adopting some recent progresses in treating atomic level interactions in proteins and nucleic acids including solvent and salt effects, we have put together an energy component methodology cast in a phenomenological mode and amenable to systematic improvements and developed a computational first atlas of the free energy contributors to binding in approximately 40 protein-DNA complexes representing a variety of structural motifs and functions. Illustrating vividly the compensatory nature of the free energy components contributing to the energetics of recognition for attaining optimal binding, our results highlight unambiguously the roles played by packing, electrostatics including hydrogen bonds, ion and water release (cavitation) in protein-DNA binding. Cavitation and van der Waals contributions without exception favor complexation. The electrostatics is marginally unfavorable in a consensus view. Basic residues on the protein contribute favorably to binding despite the desolvation expense. The electrostatics arising from the acidic and neutral residues proves unfavorable to binding. An enveloping mode of binding to short stretches of DNA makes for a strong unfavorable net electrostatics but a highly favorable van der Waals and cavitation contribution. Thus, noncovalent protein-DNA association is a system-specific fine balancing act of these diverse competing forces. With the advances in computational methods as applied to macromolecular recognition, the challenge now seems to be to correlate the differential (initial vs. final) energetics to substituent effects in drug design and to move from affinity to specificity.

Role of hydrogen bonds in protein-DNA recognition: a comparison of generalized born and finite difference Poisson-Boltzmann solvation treatments

Hydrogen bonds have been accredited with a major role historically, in the formation and stabilization of biomolecular structures. The formation of hydrogen bonds at protein-DNA interfaces in aqueous medium involves not only favorable interactions of the donor and acceptor functional groups but also a loss of interactions between these groups with the solvent water. We have investigated the energetics of about 500 potential hydrogen bonds occuring at protein-DNA interfaces incorporating some recent improvements in biomolecular force fields and solvation treatments. We present here results of our assessment of hydrogen bond contributions to the overall standard free energy of formation of protein-DNA complexes obtained with the generalized Born model and finite difference Poisson-Boltzmann methodology for solvation in conjunction with AMBER force field. Our results support the emerging view on the role of electrostatics in general and that of hydrogen bonds in particular which is that hydrogen bonds do not drive protein-DNA complex formation by virtue of the unfavourable cost of the electrostatics of desolvation. They however, act to stabilize the complex once it is formed.

Utilization of rural maternity delivery services in Nawalparasi and Kapilvastu District: A Qualitative Study

Increasing the proportion of births attended by skilled health providers is likely the key factor in reducing maternal and perinatal morbidity and mortality. Study objectives were to identify key factors influencing the utilization delivery services and stakeholders’ perceptions about these services. The study utilized focus group discussions and in-depth interviews with a diversity of community members users and nonusers , dalit women and health facility staffs to gain insights about the factors influencing use of trained attendants. Field researchers were trained to use FGD guides and interview schedules, and then gathered information on the perspectives of the women and their families and health staff. In Nawalparasi and Kapilvwastu we conducted a comparative study to compare on factors affecting the volume of delivery services.In Nawalparasi the deliveries in the pervious six months was relatively large number from hospital and PHCC whereas in Kapilvastu the delivery was in smaller number. The vast majority of women planned to have a home delivery attended by relatives and/or a Trained Birth Attendants and to reserve attendance at a health facility as a back-up plan in case of prolonged labor and complications. Ritual pollution considerations interfere with a decision to seek delivery in a facility, especially in the Western Hills. The cost recovery scheme ("incentives") deals with a major factor which inhibits use of health facilities. TBAs can encourage clients to deliver in health facilities. Staff feel that the large number of vacant positions inhibits availability of services and requires strenuous efforts on their part to cover for vacancies. Key Words: Maternity; delivery; health staff DOI: 10.3126/jcmsn.v6i3.4072Journal of College of Medical Sciences-Nepal, 2010, Vol. 6, No. 3 pp.29-36